Vol. 66, No. 1: Spring 2014

Chemical Information Bulletin

A Publication of the Division of Chemical Information of the ACS

Volume 66 No. 1 (Spring) 2014

Vincent F. Scalfani, Editor
University of Alabama, Tuscaloosa
vfscalfani@ua.edu

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Cover image is courtesy of flickr user Nick Oberheiden (creative commons license)

ISSN: 0364-1910
Chemical Information Bulletin,
©Copyright 2014 by the Division of Chemical Information of the American Chemical Society.

Message from the Chair

Greetings from snowy Philadelphia!

Judith Currano

As I attempted to write this, my first letter as chair of CINF, I found myself at a bit of a loss as to how to proceed.  Being an expert in chemical information retrieval, I immediately went to the CIB archive and read the letters of other new chairs.  I was treated to a series of fascinating perspectives on the challenges and opportunities facing chemical information professionals and informaticians.  Some past chairs felt daunted by the challenges our profession faces, while others were excited.  While I would like to present you with an insightful and inspirational discourse on the future of our profession, I fear that I am a pragmatist who thrives on day-to-day operations and, most importantly, on structure (or, as anyone who has heard me speak at a national meeting can verify, on substructure). Therefore, allow me to present my view of the structure of our division.

Every structure needs a strong core, and ours is the wonderful network of chemical information professionals around the world.  My goal this year is actively to engage as many of you as possible in division activities so that we can learn from one another and build wonderful things together.  We all know that personal and professional time commitments, travel funding that is outstripped by the cost of attending meetings, and changing job priorities frequently prevent our members from attending as many national meetings as they might otherwise like.  We are not alone; according to the statistics quoted at the last several ACS Council meetings, only about 7-10% of the Society’s members attend each conference.  We need to continue to build opportunities for our members to network, share information, and become involved in CINF activities from their offices and places of work. CINF has been ahead of the curve on this; we were one of the first divisions to record national meeting symposia and offer them as a benefit to our members.  Now, ACS offers “Presentations on Demand,” recordings of a smattering of symposia across all of the divisions, as a benefit to all Society members.  The presentations will be posted after the meeting, and I encourage conference attendees and non-attendees, alike, to peruse them. Erin Bolstad and the Program Committee have done a fantastic job of generating ideas for interesting symposia, and I hope as many people as possible can take advantage of them.

The functional groups of our division are the CINF committees. This is where we do the day-to-day business of our division. This year, I would like you to join me in invigorating one of our committees by getting involved.  While some CINF committees do meet at national meetings, most are doing a great deal of work remotely, and you will be hearing from the committee chairs throughout the year as they recruit members, describe upcoming projects, and request your assistance, wherever you happen to be.  I am particularly pleased to be working closely with the Membership and Careers Committees, (headed by Greg Banik/Donna Wrublewski and Susan Cardinal/Pamela Scott, respectively) to serve you, our members, and to highlight the kinds of work that you do to the rest of the Society.

I already know many of you, but I don’t know everyone, and I’d love to change that.  While national meetings serve as one of many opportunities for us to come together as a division and discuss our science, I found that I learned a great deal from a geographically diverse collection of CINF colleagues long before I had ever attended one.  During the coming year, let us continue to explore innovative, “non-traditional” methods of networking and exchanging ideas. I want to learn what kinds of research and work you do and hear first-hand what excites you about our profession and why you value your CINF membership.  Finally, let us work together to extend CINF’s programming activities beyond the national meetings by offering programs at the regional and local level, partnering with sister organizations, and continuing our Webinar series.  If you are aware of any opportunities, please let me know!  Although you may not have access to my office door, my e-mail inbox is always open!

Wishing you the best,

Judith Currano,
Chair, ACS Division of Chemical Information,
currano@pobox.upenn.edu

 

Letter from the Editor

Thanks for reading the ACS Chemical Information Bulletin (CIB). I would like to take this opportunity to welcome Teri Vogel to the CIB. Teri is the new Assistant Editor and has proven to be a great asset to the CINF division. She has helped tremendously with compiling and editing this issue of the CIB. Thanks Teri! I would also like to thank everyone who submitted content and assisted with the production of the CIB. Thank you for taking the time out of your busy schedules.

The completion of the CIB means two things for me. First, it brings me great joy that we completed the CIB on time! But more importantly, it means that it is time to get ready for Dallas. Skimming through the technical program, I see many familiar names and many unfamiliar names. I am very much looking forward to catching up with you or meeting you for the first time. I’ll see you in Dallas!

Vincent F. Scalfani, Editor
vfscalfani@ua.edu

 

Letter from the Assistant Editor

Welcome to the latest issue of the Chemical Information Bulletin (CIB). At the Indianapolis meeting, Tony Williams put out a call for people to help with CIB. I contacted him after the meeting to express interest, followed up with David Martinsen, and here I am. As one of the new assistant editors, I will be helping Vincent F. Scalfani with the pre-conference spring and fall issues.

While I did sign on as a way to increase my involvement in CINF, I also wanted to push myself to write more. And reading, along with proofreading and editing, other people’s work inspires me to stop procrastinating and start writing. The deadlines help as well.

In this issue you’ll find the technical program, abstracts, and business and social events for the upcoming ACS Meeting in Dallas. We also have book reviews and a career planning article, plus “Topics of Interest” submissions from Bob Buntrock and Tina Qin.

Would you like to write for a future issue of CIB? Write about what you’re reading (books, articles, blogs, etc.) or what topics you recently searched. Perhaps you’ve come across a new resource, or a new way to teach or promote information resources to your users. Or you attended another conference that other CINF members would find interesting, and you want to share what you learned with the rest of us. Maybe there’s something you think you’d like to write about, but you want to bounce ideas off someone. If any of these apply, or you have additional questions about contributing for CIB, please contact me.

Teri Vogel, Assistant Editor
tmvogel@uscd.edu

 

Social Networking & Business Events

Social Networking Events

  • 2476 reads

ACS CINF Social Networking Events at the Spring 2014 ACS Meeting

 

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Please Join Us at these
Division of Chemical Information Events!

The ACS Division of Chemical Information is pleased to host the following social networking events at the Spring 2014 ACS National Meeting in Dallas, TX.

Sunday, March 16th

Monday, March 17th

  • Harry’s Party
    5:30-8:00 pm
    Sheraton Dallas, Suite Location TBA
    (Shuttle route 2 (1 mile)).

Tuesday, March 18th

Committee Meetings

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ACS CINF Business Events at the Spring 2014 ACS Meeting

Saturday, March 15, 2014

  • 1:00 PM - 3:00 PM CINF Awards Meeting. Deep Ellum B, Omni Dallas Hotel
  • 1:00 PM - 3:00 PM CINF - Education Committee. Arts District 4, Omni Dallas Hotel
  • 1:00 PM - 3:00 PM CINF - Program Committee. Deep Ellum A, Omni Dallas Hotel
  • 3:00 PM - 6:00 PM CINF - Executive Committee. Katy Trail, Omni Dallas Hotel

Sunday, March 16, 2014

  • 12:00 PM - 2:00 PM CINF - CSA Trust. Arts District 4, Omni Dallas Hotel

 

Awards and Scholarships

CSA Trust

  • 2045 reads

CSATrust

 

Applications Invited for CSA Trust Grants for 2014 and 2015

The Chemical Structure Association (CSA) Trust is an internationally recognized organization established to promote the critical importance of chemical information to advances in chemical research.  In support of its charter, the Trust has created a unique Grant Program and after March 13, 2014 will be inviting the submission of grant applications for 2015. The call for the 2014 Grant is open until March 13, 2014.

Purpose of the Grants

The Grant Program has been created to provide funding for the career development of young researchers who have demonstrated excellence in their education, research or development activities that are related to the systems and methods used to store, process and retrieve information about chemical structures, reactions and compounds.  One or more Grants will be awarded annually up to a total combined maximum of ten thousand U.S. dollars ($10,000). Grants are awarded for specific purposes, and within one year each grantee is required to submit a brief written report detailing how the grant funds were allocated. Grantees are also requested to recognize the support of the Trust in any paper or presentation that is given as a result of that support.

Who is Eligible?

Applicant(s), age 35 or younger, who have demonstrated excellence in their chemical information related research and who are developing careers that have the potential to have a positive impact on the utility of chemical information relevant to chemical structures, reactions and compounds, are invited to submit applications. While the primary focus of the Grant Program is the career development of young researchers, additional bursaries may be made available at the discretion of the Trust. All requests must follow the application procedures noted below and will be weighed against the same criteria.

Which Activities are Eligible?

Grants may be awarded to acquire the experience and education necessary to support research activities, for example, for travel to collaborate with research groups, to attend a conference relevant to one’s area of research, to gain access to special computational facilities, or to acquire unique research techniques in support of one’s research.

Application Requirements

Applications must include the following documentation:

  1. A letter that details the work upon which the Grant application is to be evaluated as well as details on research recently completed by the applicant;
  2. The amount of Grant funds being requested and the details regarding the purpose for which the Grant will be used (e.g. cost of equipment, travel expenses if the request is for financial support of meeting attendance, etc.). The relevance of the above-stated purpose to the Trust’s objectives and the clarity of this statement are essential in the evaluation of the application);
  3. A brief biographical sketch, including a statement of academic qualifications; 
  4. Two reference letters in support of the application.  Additional materials may be supplied at the discretion of the applicant only if relevant to the application and if such materials provide information not already included in items 1-3. Three copies of the complete application document must be supplied for distribution to the Grants Committee.

Deadline for Applications

Applications for the 2014 Grant must be received no later than March 13, 2014.  The date for the 2015 Grant is March 13, 2015. Successful applicants will be notified no later than May 2nd of the relevant year.

Address for Submission of Applications: 

Three copies of the application documentation should be forwarded to:  Bonnie Lawlor, CSA Trust Grant Committee Chair, 276 Upper Gulph Road, Radnor, PA 19087, USA.  If you wish to enter your application by e-mail, please contact Bonnie Lawlor at blawlor@nfais.org prior to submission so that she can contact you if the e-mail does not arrive.

 

Chemical Structure Association Trust:  Recent Grant Awardees

2013 – Dr. Johannes Hachmann

Department of Chemistry and Chemical Biology at Harvard University, Cambridge, MA.   He was awarded the Grant for travel to speak on “Structure-property relationships of molecular precursors to organic electronics” at a workshop sponsored by the Centre Européen de Calcul Atomique et Moléculaire (CECAM) that took place October 22 – 25, 2013 in Lausanne, Switzerland. .

2013 – Dr. Robert S. Paton

University of Oxford, UK.  He was awarded the Grant to speak at the Sixth Asian Pacific Conference of Theoretical and Computational Chemistry in Korea on July 11, 2013. Receiving the invitation for this meeting has provided Dr. Paton with an opportunity to further his career as a Principal Investigator.

2013 – Dr. Aaron Thornton

Material Science and Engineering at CSIRO in Victoria, Australia. He was awarded the Grant to attend the 2014 International Conference on Molecular and Materials Informatics at Iowa State University with the objective of expanding his knowledge of web semantics, chemical mark-up language, resource description frameworks and other online sharing tools.  He will also visit Dr. Maciej Haranczyk, a prior CSA Trust Grant recipient, who is one of the world leaders in virtual screening.

2012 – Tu C. Le

CSIRO Division of Materials Science & Engineering, Clayton, VIV, Australia. Tu C. was awarded the Grant for travel to attend a Cheminformatics course at Sheffield University and to visit the Membrane Biophysics group of the Department of Chemistry at Imperial College London.

2011 – J. B. Brown

Kyoto University, Kyoto, Japan. J.B. was awarded the Grant for travel to work with Professor Ernst Walter-Knappat the Freie University of Berlin and Professor Jean-Phillipe Vert of the Paris MinesTech to continue his work on the development of atomic partial charge kernels.

2010 – Noel O’Boyle

University College Cork, Ireland. Noel was awarded the grant to both network and present his work on open source software for pharmacophore discovery and searching at the 2010 German Conference on Cheminformatics.

2009 – Laura Guasch Pamies

University Rovira & Virgili, Catalonia, Spain.  Laura was awarded the Grant to do three months of research at the University of Innsbruck, Austria.

2008 – Maciej Haranczyk

University of Gdansk, Poland. Maciej was awarded the Grant to travel to Sheffield University, Sheffield, UK, for a 6-week visit for research purposes.

2007 – Rajarshi Guha

Indiana University, Bloomington, IN, USA. Rajarshi was awarded the Grant to attend the Gordon Research Conference on Computer Aided Design in August 2007.

2006 – Krisztina Boda

University of Erlangen, Erlangen, Germany. Krisztina was awarded the Grant to attend the 2006 spring National Meeting of the American Chemical Society in Atlanta, GA, USA.

2005 – Dr. Val Gillet and Professor Peter Willett

University of Sheffield, Sheffield, UK.  They were awarded the Grant for student travel costs to the 2005 Chemical Structures Conference held in Noordwijkerhout, the Netherlands.

2004 – Dr. Sandra Saunders

University of Western Australia, Perth, Australia. Sandra was awarded the Grant to purchase equipment needed for her research.

2003 – Prashant S. Kharkar

Institute of Chemical Technology, University of Mumbai, Matunga, Mumbai. Prashant was awarded the Grant to attend the conference, Bioactive Discovery in the New Millennium, in Lorne, Victoria, Australia (February 2003) to present a paper, The Docking Analysis of 5-Deazapteridine Inhibitors of Mycobacterium avium complex (MAC) Dihydrofolate reductase (DHFR).

2001 – Georgios Gkoutos

Imperial College of Science, Technology and Medicine, Dept. of Chemistry. London, UK. Georgios was awarded the Grant to attend the conference, Computational Methods in Toxicology and Pharmacology Integrating Internet Resources, (CMTPI-2001) in Bordeaux, France, to present part of his work on internet-based molecular resource discovery tools.

 

CINF Scholarship for Scientific Excellence

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2014 CINF Scholarship for Scientific Excellence Sponsored by the Royal Society of Chemistry

The scholarship program of the Division of Chemical Information (CINF) of the American Chemical Society (ACS) funded by the Royal Society of Chemistry (RSC) is designed to reward graduate and postdoctoral students in chemical information and related sciences for scientific excellence and to foster their involvement in CINF. 

Up to four scholarships valued at $1,000 each will be presented at the 248th ACS National Meeting in San Francisco, CA, August 10 – August 14, 2014. Applicants must be enrolled at a certified college or university, and they will present a poster during the Welcoming Reception of the Division on Sunday evening at the National Meeting.  Additionally, they will have the option to show their poster at the Sci-Mix session on Monday night.  Abstracts for the poster must be submitted electronically through PACS, the abstract submission system of ACS.

To apply, please inform the chair of the selection committee, Guenter Grethe at ggrethe@att.net that you are applying for a scholarship. Submit your abstract to http://abstracts.acs.org using your ACS ID.  If you do not have an ACS ID, follow the registration instructions and submit your abstract in the CINF program for the session “CINF Scholarship for Scientific Excellence”.  PACS will be open for abstract submissions from January 13 to March 10, 2014. Additionally, please send a 2,000-word abstract describing the work to be presented in electronic form to the chair of the selection committee by June 20, 2014.  Any questions related to applying for one of the scholarships should be directed to the same e-mail address.

Winners will be chosen based on contents, presentation and relevance of the poster and they will be announced during the reception. The contents will reflect upon the student’s work and describe research in the field of cheminformatics and related sciences.

Guenter Grethe

 

Career Resources - Plant Your Chemical Career Now

As a student, your days (and sometimes nights) are full of classes, research projects, and perhaps teaching responsibilities or another job. Graduation, and the start of your “real” career seems way off in the future. There’s plenty of time to worry about that later, when graduation looms closer. Right? Wrong. 

Even while in school, you need to invest time, thought, and effort to built your reputation and your professional network. These are the bedrocks upon which your entire professional career rest, and the earlier you start building the better off you will be. 

Start by figuring out who you want to be. Do you want to be known as an organic chemist with expertise in steroid synthesis, or an analytical chemist with expertise in HPLC? You have many different areas of expertise and knowledge, but only you can decide which are your strongest assets, and which you enjoy using and want to emphasize in the next stage of your professional career. Then, make sure to describe yourself that way when making new professional connections.  

Once you have an idea of who you want to be, let the world know by crafting your online persona (also called your personal brand). Create a professional profile on LinkedIn and the ACS Network. Go beyond just filling in the facts: join and contribute the conversation in groups that interest you, especially ones related to your technical areas of interest and expertise. Not only will you learn about current developments in your field, but by contributing useful information and opinions you will build your reputation among your fellow professionals. 

Make time every day to do something that will advance your career. Read journal articles in fields only slightly related to your research, and see what you can learn from them. Set up automatic email alerts on job boards, and track hiring trends in your field over time. Nurture your professional relationships: have lunch with someone new, email an interesting article to a distant colleague, serve on a committee, or write and publish a thoughtful blog article on new developments in your field. 

While these things are important throughout your career, you need to get even more serious about narrowing down your options 12-18 months before you need a new position, so you can have one ready when you graduate. Any gap in employment is bad, and it has been shown that your odds of finding a job go down dramatically as the period of unemployment lengthens (they drop 45% after 6 months of unemployment http://qje.oxfordjournals.org/content/128/3/1123.abstract). By narrowing your focus to what you are really excited about and qualified for, and knowing what the market is, you will be an the ideal position to put the pieces together and make a graceful transition into the next stage of your professional life.   

Think of your career as a garden  You need to plant seeds now, water and nurture them over a long time, and they will grow into beautiful plants that you can harvest later to meet your needs. This requires planning for the long term, investing significant time and energy early in the process, and then continuing to invest for as long as you want to be able to harvest. 

 

ACS Resources:

 

Other Resources

 

Job Search Engines

  • LinkUp  (linkup.com) – gets postings directly from companies
  • Indeed (indeed.com) – aggregates results from many other search engines

 

Publications

 

Professional Societies

  • American Society for Indexing (http://www.asindexing.org) - professional organization devoted to the advancement of indexing, abstracting, and database building
  • American Society for Information Science and Technology (ASIST) (asis.org) - society for information professionals leading the search for new and better theories, techniques, and technologies to improve access to information
  • Association of American Publishers (publishers.org) - trade association of the book publishing industry
  • Association of Independent Information Professionals (aiip.org) - provides a wealth of resources for those who want to know more about the information industry and independent information professionals
  • NFAIS (nfais.org) - serves groups that aggregate, organize, and facilitate access to information
  • Society for Scholarly Publishing (sspnet.org) - works to advance scholarly publication and communication and the professional development of its members
  • Patent Information Users Group (PIUG) (piug.org) - Organization for patent professionals.  The web site has great links and the discussion list is free to join.  Many companies advertise patent searching positions on their discussion list.

 

This article was written by Lisa M. Balbes, Ph.D. of Balbes Consultants LLC.  Lisa is a freelance technical writer/editor and author of: “Nontraditional Careers for Chemists:  New Formulas for Chemistry Careers,” published by Oxford University Press.

 

 

 

Book Reviews

A Tale of Seven Elements

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Scerri, Eric. A Tale of Seven Elements. Oxford University Press, Oxford. 2013. ISBN-10: 0195391314. Price: $18.95

Does it really matter who has made a particular discovery? In his book, “A Tale of Seven Elements,” Eric Scerri shows that it does, at least to the scientists involved in it (E. Scerri, 2013). The book is about how seven elements with atomic numbers in the range from 43 to 91 were isolated and identified.  The discovery of protactinium (Pa), hafnium (Hf), rhenium (Re), technetium (Tc), francium (Fr), astatine (At), and promethium (Pm) are discussed in the context of the historical events between and during the two world wars. This background allows the reader to appreciate the human side of the efforts and personal sacrifices made by the scientists. It is hard for the contemporary reader to even imagine what it looked like to continue to work when tragic events such as persecution of ethnic groups, nationalism, and killing of innocent people were raging outside the lab.

The book is a continuation of the author’s interest in the history of the Periodic Table. The first two chapters are a concise version of his previous book, “The Periodic Table: Its Story and Its Significance” (E. R. Scerri, 2006), which is the most comprehensive account of how Dmitri Mendeleev and other scientists came to create an organized system for arranging the chemical elements and were even able to predict such that were not yet discovered. More recently, Scerri has also published a smaller book on the periodic table (E. Scerri, 2012).

Several years ago I interviewed Dr. Scerri about his research and the interview was published in the Chemical Information Bulletin (Baykoucheva, 2010).  In his new book I could see some of the themes he discussed in this interview: the nature of research, the personal struggles of scientists, their disputes about priority and recognition, and what it has cost (in terms of human effort and sacrifice) to discover a new chemical element.

Seven chapters in the book reviewed here are devoted to the individual elements, and another chapter follows the research devoted to filling the open spaces for missing elements and the synthesis of new elements. When he drew his version of the Periodic Table, Mendeleev predicted the existence of three of the seven elements discussed in the book—technetium, astatine, and promethium, but it took many years before these elements were actually isolated and confirmed. Some of the seven elements were first synthesized in the lab and then isolated from natural materials. Four of them exist only in trace amounts in the Earth’s crust, and their discovery required processing huge amounts of raw materials. To obtain only 125 g of protactinium, the Atomic Energy Authority in the United Kingdom processed 60 tons of waste of uranium minerals, spending $500,000 for this purchase. The product was later sold at the price of $3,000 per gram, but the element itself found no applications in real life except for studying the age of ancient oceans.

Scerri emphasized the significance of the work of the English scientist Henry Mosley who suggested that the chemical elements should be ordered as a sequence of integers (later called atomic numbers), rather than by atomic weight, as it was initially proposed by Mendeleev. This arrangement made it possible to explain many observed discrepancies and gaps in the periodic table. It was the X-ray method that he discovered that led to the identification of several new chemical elements and has allowed others to predict precisely the elements that remained to be isolated.

The book of Eric Scerri is about the successes and failures in discovering these seven chemical elements, and it raises many interesting questions about how discoveries are made. Scientists often argue about priority and the significance of their work, with nationalism and personal rivalries contributing to the complexity of the process.  Does a discovery need to be announced in a reputable scientific journal? (For example, the discovery of palladium by William Hyde Wollaston was announced in a newspaper advertisement.) This question is very relevant today, when new forms of scholarly communication and social networking tools allow scientists to bypass the traditional ways of publishing.

Scerri shows how difficult it has been to determine who should get the credit for a particular discovery. There were cases when an element was isolated but remained unknown until someone else identified and published it. Other elements, including carbon and sulfur, have been discovered anonymously, as were all the elements that were discovered before the year 1500. Also, a discovery may be attributed to more than one person or a group of people, as the same research is usually carried out in different labs and different countries. 

Although the book is about seven rare elements, the personal stories of the scientists behind these discoveries and the historical background on which these events played out contribute significantly to the enjoyment of reading it. I cannot look at the book through the eyes of someone who has never studied chemistry, but I am sure that those interested in the history of science will find interesting information in it that is not so difficult to understand.  To me, the book was not only a useful refresher of how the periodic table came into being, and how scientists pursued the discovery of the individual elements.  I have learned a lot of interesting facts that have somehow evaded my attention before.

References

  • Baykoucheva, S.  A philosopher’s view on the periodic table of the elements and its significance: Interview with Eric Scerri. Chemical Information Bulletin, 2010, 62(1), 16-21, http://hdl.handle.net/1903/11845.
  • Scerri, E. R. The Periodic Table: A Very Short Introduction. Oxford University Press, Oxford, England, 2012.
  • Scerri, E. R.  A Tale of Seven Elements: Oxford University Press, Oxford, England, 2013.
  • Scerri, E. R. The Periodic Table: Its Story and Its Significance: Oxford, England, 2006.

 

Svetla Baykoucheva
White Memorial Chemistry Library
University of Maryland College Park
sbaykouc@umd.edu 

 

Chemical Information for Chemists

  • 2757 reads

Currano, Judith N., Roth, Dana L., eds. Chemical Information for Chemists; A Primer.  RSC Publishing, Cambridge, UK, 2014: pp. 1-306 + xv, ISBN 978-1-84973-551-3 (softcover), (GDP 24.99) ($54/34 Amazon)

This book is an essential resource for chemical information for chemists and other researchers as well as an up-to-date reference, and teaching tool, for science librarians and information specialists.  Multi-authored by experts in their fields, it covers a wide scope of topics.  Both “classical” (i.e. print) and digital/electronic sources are discussed and access methods are described.  Resources that are free are distinguished from those that are fee-based.  References are at the end of each chapter, and an index to all material concludes the book.

Leading off is the introduction by Leah McEwen.  The nature and history of chemical information is outlined.  The importance of quality information is stressed, including the need for archiving and information professionals as well as for searching and reading by scientists.  Dana Roth begins the Primary Literature Section with a chapter on the non-patent literature of chemistry.  Journals, abstracting and indexing resources, open access, current awareness, impact factors, and gray literature are described.  Michael White opens the next chapter, Chemical Patents, with an excellent, concise description of patents in general, exemplary for chemical patents and sources for chemical patent information.  Intellectual Property in general is discussed, and the frustrating variability in both author and organization names is extensively described.

The Secondary Literature and Search Techniques Section begins with Andrea Twiss-Brooks’ chapter titled Searching Using Text: Beyond Search Engines. She describes the insufficiency of the latter, as well as basics like precision, recall, word variants, nomenclature, author names, and citation.  Judith Currano’s chapter on structure and substructure searching is quite comprehensive and covers a number of resources with SciFinder and Reaxys highlighted.  Detailed strategies for a number of search topics are presented.  Ben Wagner next thoroughly describes physical properties and spectra.  The wealth of sources of such data in both print and electronic formats is listed and described.  Dana Roth follows with another excellent chapter on commercial availability, safety, and hazards (including toxicity), with detailed descriptions of the information resources on these topics.

Donna Wrublewski not only describes sources of information and data on polymers, but she also begins with an introduction on polymers in general.  Judith Currano follows with another excellent chapter on chemical reaction searching, again with an emphasis on SciFinder and Reaxys.  Diane Rein concludes with a chapter titled A Practical Primer to BLAST Sequence Similarity Searching.  I have never done this type of searching, so I must assume this chapter covers the topic well (which I am sure it does).

The need for well stocked and staffed chemistry libraries is obvious given the extent of valuable sources available only by purchase or subscription.  The chapter material in several cases has evolved from teaching done by the authors.  Where applicable, the emphasis is on SciFinder and Reaxys, to meet the anticipated needs of the intended audience.  In a few cases, comparisons are made to chemistry files on STN, but the power of STN for several kinds of searching, including patents and polymers, is not described.  Polymer description and searching is even more complicated than is discussed in Chapter 8. While the authors’ affiliations are listed, there is no mention of their credentials like educational background or professional experience. Some readers will certainly be familiar with the authors and their authority on these topics, but other readers such as those are not science librarians and chemical information professionals may not.

These are minor quibbles and the book is highly recommended for chemists, chemistry students, and their teachers.  It should be available in all chemistry libraries as well as personal libraries of chemists and as a text for chemical information courses.

Disclaimer: although I know or have met the majority of the authors, this reinforces my perception of their expertise and has not unduly affected my review.

There are discrepancies in the listings for this book.  The RSC website listed the publication date as Feb. 1, 2013, since corrected to 2013.  The Amazon posting is Oct. 22, 2013, but the title page on my copy is 2014.  According to the RSC site, it is included in the RSC eBook Collection.

Bob Buntrock
Orono, ME
buntrock16@roadrunner.com

CINF Reader Submitted Chemical Information Topics of Interest

Sources of Information

  • 2162 reads

by Bob Buntrock, Orono, ME

Since the searching part of my consultancy is inactive, most of my research is self-funded, so I take advantage of free sources or limited free access generously granted.  Two new free resources available to ACS members are limited access to SciFinder (25 activities annually) and free downloads from any of the ACS journals (also 25 annually). I have not yet taken advantage of the free look and download of “the article of the day”.

I have never had access to SciFinder before, so my first foray was a comparison of searching of SciFinder and Reaxys.  Elsevier granted me limited access to Reaxys. The topic I searched was the estrogenic activity of resveratrol, especially on estrogen receptors. I do not have modeling and docking programs available, but by its structure resveratrol looked like it would have estrogenic activity.  It does. The results of my study have been published in Online Searcher (http://www.infotoday.com/OnlineSearcher/Articles/InDepth-Reports/Apples-and-Oranges-A-Chemistry-Search-Compares-CAS-SciFinder-and-Elseviers-Reaxys-91663.shtml).  I have also used SciFinder to search for preparations of Tamoxifen, information not that readily available.

I’ve previously described that if one suspends a subscription to an ACS journal, then one loses access to the electronic back file. This is especially onerous for that period when the electronic version was the only one available. I used my 2013 quota of downloads to retrieve my publications in JCICM and JCICS. I have a few more to go with my 2014 quota, including a few publications in other journals.

Due to presentations by Martin Walker, I have been impressed with the quality of chemical information and data in Wikipedia.  Via Martin and the Chemistry Editing Group, I have already updated one article and I plan more authorship and updates.

Both the accuracy and currency of chemistry in Wikipedia was recently exemplified through tracking down information on toxicity and health effects on MCHM, also known as methylcyclohexanemethanol, the chemical spilled recently in West Virginia. Noting the lack of information on identity and hazards expressed in articles in both ACS Industry Notes and C&EN, I had been checking out the usual sources like Merck Index and Sax to no avail. Searching Wikipedia yielded a currently updated article, including citations to the spill and follow-up, plus data including the CAS RN (34885-03-5). Reference was also made to PubChem with the PubChem compound number. Searching that yielded more data plus links to TOXNET and HSDB.  The latter had a current article on human health effects along with links to Eastman Chemical data.  I reported these results on the recent MCHM string on CHMINF-L.  All access was free.  Again, the need for CAS RN in chemical identification is paramount since there were problems with nomenclature by the first responders, cleanup staff, and journalists.

Exploring EndNote beyond “Export”

  • 1854 reads

by Tina Qin, Michigan State University

Researchers increasingly work with EndNote, Mendeley, Zotero and other citation management tools. All of the citation managers are intended to provide the same basic features and functionality with a few exceptional scenarios.

Most chemistry researchers at Michigan State University use EndNote Desktop for their own research, and our library offers free EndNote training classes. An EndNote library can be a good literature manager since it can organize reference citations and attach the original PDF file directly to the reference. Before such a citation management tool was available, researchers were forced to download files, rename them, and then save the file in a known folder on their personal computer.

Many users assume the easiest way to collect sources from various databases is to simply click the “export” button and then save within their reference database. However, citation management tools can maximize their use in other ways beyond this “export” button.

For example, I recently received a request about organizing chemistry professors’ publications for their tenure-track faculty evaluation. I found EndNote would be a good tool to fulfill this duty. In exporting citations, EndNote works seamlessly with Web of Science and is compatible with SciFinder and Reaxys. Researchers who do not share the same EndNote library can even collaborate on a paper because the formatted citations include embedded reference data to function as a “traveling library.” In this evaluation process, a number of faculty members communicated with me on adding or dropping references in the traveling library I created. EndNote, an efficient and productive citation management tool has been widely used in our chemistry department.

We know that there are plenty of citation management tools out there, with some offering additional functionality like cloud storage, PDF annotation, and social networking. Further exploration of how these tools are expanding, and what we expect of reference managers would be beneficial to librarians who are looking to develop additional roles that provide campus-wide research services.

 

Notes From Our Sponsors

CINF Sponsors Spring 2014

  • 1799 reads

Image                    Image

Division of Chemical Information Sponsors

Spring 2014

The American Chemical Society Division of Chemical Information is very fortunate to receive generous financial support from our sponsors to maintain the high quality of the Division’s programming and to promote communication between members at social functions at the ACS Spring 2014 National Meeting in Dallas, Texas, and to support other divisional activities during the year, including scholarships to graduate students in Chemical Information. The Division gratefully acknowledges contribution from the following sponsors:

Gold:

Silver:

Bronze:

Contributors:

Opportunities are available to sponsor Division of Chemical Information events, speakers, and material. Our sponsors are acknowledged on the CINF web site, in the Chemical Information Bulletin, on printed meeting materials, and at any events for which we use your contribution. For more information please review the Sponsorship Brochure at http://www.acscinf.org/PDF/Fundraising_Brochure.pdf.

Please feel free to contact me if you would like more information about supporting CINF.

Phil Heller, Chair, Fundraising Committee
Email: Fundraising AT acscinf.org
Tel: 917-450-4591

The ACS CINF Division is a non-profit tax-exempt organization with taxpayer ID no. 52-6054220.

CAS and PerkinElmer Collaborate

  • 2399 reads

Chemical Abstracts Service (CAS) and PerkinElmer Collaborate to Enhance the Efficiency of Researchers’ Workflows — December 9th, 2013

CAS

Chemical Abstracts Service (CAS), the world’s authority for chemical information, and PerkinElmer, Inc., a global leader focused on improving the health and safety of people and the environment, today announced a collaboration to combine the power of two leading chemistry solutions: SciFinder and ChemBioDraw.

The ChemBioDraw platform is a digital drawing tool for chemists and biologists to create publication-ready, scientifically intelligent drawings for use in ELNs, databases and publications. SciFinder is a research discovery application that provides integrated access to the world’s most comprehensive and authoritative source of references, substances and reactions in chemistry and related sciences, which are collected, organized and indexed by CAS scientists.

New functionality is being developed to enable a ChemBioDraw user to directly initiate a search in SciFinder, providing access to comprehensive content available in the CAS databases. The integrated solution is planned to be available in early 2014.

“Combining the power of two leading chemistry platforms will enable researchers to more efficiently progress in their workflows,” said Clive Higgins, Vice President of Informatics Marketing, PerkinElmer. “The drawing capabilities in the ChemBioDraw platform are used across a large installed base, and adding the SciFinder search capability within the ChemBioDraw solution will extend the access to this authoritative chemical information from CAS.”

PerkinElmer

“CAS is pleased to collaborate with PerkinElmer to address the latest research challenges facing chemists, biologists and other scientists,” said Chris McCue, Vice President of Marketing at CAS. “We recognize that our users need integrated workflows that save them time and enhance discovery.  Seamless access between SciFinder and the ChemBioDraw platform builds on impressive histories of excellence, customer service and innovation from both organizations.”

For more information on SciFinder and CAS content, visit www.cas.org.

For more information on PerkinElmer’s informatics solutions visit www.perkinelmer.com/informatics/.

 

Media Contacts

Rhonda Ross
CAS
Email: mailto:cas-pr@cas.org

Fara Goldberg
PerkinElmer
Email: fara.goldberg@perkinelmer.com

 

About CAS

Chemical Abstracts Service (CAS), a division of the American Chemical Society, is the world’s authority for chemical information. CAS is the only organization in the world whose objective is to find, collect and organize all publicly disclosed substance information. A team of scientists worldwide curates and controls the quality of our databases, which are recognized as the most comprehensive and authoritative by chemical and pharmaceutical companies, universities, government organizations and patent offices around the world. By combining these databases with advanced search and analysis technologies (SciFinder and STN), CAS delivers the most current, complete, secure and interlinked digital information environment for scientific discovery.

About PerkinElmer, Inc.

PerkinElmer, Inc. is a global leader focused on improving the health and safety of people and the environment. The company reported revenue of approximately $2.1 billion in 2012, has about 7,500 employees serving customers in more than 150 countries, and is a component of the S&P 500 Index. Additional information is available through 1-877-PKI-NYSE, or at www.perkinelmer.com.

Source:
https://www.cas.org/news/media-releases/cas-and-perkinelmer-collaborate

 

 

InfoChem News

  • 1841 reads

New ICEDIT web version released

icedit

InfoChem is pleased to announce the release of a new ICEDIT web version. This new version of InfoChem’s drawing and depicting tool is based on JavaScript and is HTML5 compatible. This allows flexible integration in all standard browsers, avoiding security issues with Java applets.

Click here for more information about ICEDIT and to test the JavaScript version.

 

Name Reaction search to be included in SPRESImobile App

InfoChem is pleased to announce a new release of SPRESImobile in March 2014. The free App for iPhone and iPad is developed to perform structure and reaction searches on mobile devices and offers access to more than 500K reactions - these are a subset of the SPRESI reaction data (ChemReact). Additionally, SPRESIweb subscribers have access to the entire SPRESI reaction content.

spresimobile app

Name Reaction searching will be integrated in the new App version. After registration users will be able to see a new button for name reaction searches in the reaction search form. Furthermore, all users (including those not registered) will see a new hyperlink with the Name Reaction in the reaction hit list, when named reactions are hits for a reaction search. This hyperlink allows users to retrieve all reactions assigned to the specific mechanism.

For more information about SPRESImobile please click here.

Please feel free to contact us for more information about InfoChem, our current research projects and our products.

Technical Program

Symposia

  • 2784 reads

ACS Chemical Information Division (CINF)
247th ACS National Meeting, Spring 2014
Dallas, TX (March 16 - 20)

CINF Symposia

E. Bolstad, Program Chair

S M T W T Session title
A         Joint CINF-RSC CICAG Symposium: Chemical Schemas, Taxonomies and Ontologies - AM Session Ontologies and Substances**
A         Joint CINF-CSA Trust Symposium: Energy Information Resources to Help Catalyze Your Research
P         Joint CINF-RSC CICAG Symposium: Chemical Schemas, Taxonomies and Ontologies**
P         Translational Cancer Bioinformatics: Data, Methods and Applications**
P         Neglected and Rare Disease Drug Discovery Needs Open Data
E         CINF Scholarship for Scientific Excellence
  A       Keeping the Thrill Alive: Research Data and Electronic Notebooks**
  P       Keeping the Thrill Alive: Research Data and Electronic Notebooks**
  E       Sci-Mix
    A     Ethical Considerations in Digital Scientific Communication and Publishing**
    P     Cloud Computing in Cheminformatics**
      A   New Models in Substance Discovery
      P   General Papers

Symposia co-sponsored by CINF

Selecting a co-sponsored symposium will take you outside of the current Committee, Secretariat or Division

S M T W T Session title
      D   Mobile Devices, Augmented Reality, and The Mobile Chemistry Classroom*(CHED)
    D     ACS Award for Computers in Chemical and Pharmaceutical Research: Symposium in Honor of Martin Stahl*(COMP)
      P   Computational Approaches To Spectroscopy Analysis*(COMP)
A         Computational Study of Water*(COMP)
D D   D   Drug Discovery*(COMP)
    D A   Material Science*(COMP)
  A       Membranes*(COMP)
P P P D   Molecular Mechanics*(COMP)
    E     Poster Session*(COMP)
D D D D   Quantum Chemistry*(COMP)
D D A     Tracing Pathways in Biomolecular Simulation*(COMP)
  A       Benefits of Chemistry in our Lives*(PRES)

 

Legend:
A = AM, P = PM, D = AM/PM, E = Evening
*Cosponsored symposium with primary organizer shown in parenthesis; located with primary organizer.
**Primary organizer of cosponsored symposium.

See also: Complete Program

Technical Program Listing

  • 12597 reads

ACS Chemical Information Division (CINF)
247th ACS National Meeting, Spring 2014
Dallas, TX (March 16-20, 2014)

CINF Symposia

E. Bolstad, Program Chair

Sunday, March 16, 2014

Joint CINF-RSC CICAG Symposium: Chemical Schemas, Taxonomies and Ontologies - AM Session Ontologies and Substances
Omni Dallas Hotel
Room: Deep Ellum A
Cosponsored by COMP, MEDI, ORGN, PHYS
Antony Williams, Jeremy Frey, Simon Coles, Leah McEwen, Organizers
Jeremy Frey, Presiding
8:30 am - 11:55 am
8:30   Introductory Remarks
8:45 1 Bridging worlds: Speaking multiple scientific languages

Jessica Peterson1, J.Peterson@elsevier.com, Pieder Caduff2, David Evans2, Juergen Swienty-Busch3.
Abstract
9:10 2 Ontology-driven information system for chemical and materials science

Nico Adams1, nico.adams@csiro.au, Murray Jensen1, Danielle Kennedy1, Cornelius Kloppers2, Yanfeng Shu2, Claire D'Este2, Craig Lindley2.
Abstract - No slides available
9:35 3 Open ontologies and chemical characterization

Colin Batchelor1, Leah R McEwen2, lrm1@cornell.edu.
Abstract - Slides (pdf)
10:00   Intermission
10:15 4 FDA terminology for substances

Yulia Borodina, yulia.borodina@fda.hhs.gov, Larry Callahan, Frank Switzer, Bill Hess, Randy Levin.
Abstract - Slides (pdf)
10:40 5 Pipeline for automated structure-based classification in the ChEBI ontology

Janna Hastings, hastings@ebi.ac.uk, Venkatesh Muthukrishnan, John W May, Gareth Owen, Christoph Steinbeck.
Abstract
11:05 6 Accessing Open PHACTS: Interactive exploration of compounds and targets from the semantic web

Katrin Stierand1, stierand@zbh.uni-hamburg.de, Tim Harder3, Lothar Wissler2, Christian Lemmen2, Matthias Rarey1.
Abstract
11:30 7 Machine-processable representation and applications of the Globally Harmonized System

Mark I Borkum, m.i.borkum@soton.ac.uk,
Abstract - Slides (pdf)

Sunday, March 16, 2014

Joint CINF-CSA Trust Symposium: Energy Information Resources to Help Catalyze Your Research - AM Session
Omni Dallas Hotel
Room: Deep Ellum B
Grace Baysinger, Organizers
Grace Baysinger, Presiding
8:30 am - 11:55 am
8:30   Introductory Remarks
8:35 8 Trends in bio-based chemicals: Business intelligence from published literature

Steve M Watson, s.watson@elsevier.com,
Abstract - Slides (pdf)
9:05 9 Chemistry databases and alerting services for finding the best energy research content

Serin Dabb1, dabbs@rsc.org, Richard Kidd2.
Abstract - Slides (pdf)
9:35 10 Sustainable chemistry in the CAS databases

Cristian Dumitrescu1, cdumistrescu@cas.org, Roger Schenck2.
Abstract - Slides (pdf)
10:05   Intermission
10:20 11 Fading shades of gray? ACS Meeting preprints past, present, and future

David Flaxbart, flaxbart@austin.utexas.edu,
Abstract - Slides (pdf)
10:50 12 On the fly collection development to support emergent energy research initiatives

Donna T. Wrublewski, dtwrublewski@library.caltech.edu, George Porter, Dana Roth.
Abstract - Slides
11:20 13 X marks the spot: Using xSearch for discovering energy information

Grace Baysinger, graceb@stanford.edu,
Abstract - Slides (pdf)
11:50   Concluding Remarks

Sunday, March 16, 2014

Joint CINF-RSC CICAG Symposium: Chemical Schemas, Taxonomies and Ontologies - PM Session Platforms and Processes
Omni Dallas Hotel
Room: Deep Ellum A
Cosponsored by COMP, MEDI, ORGN, PHYS
Leah McEwen, Antony Williams, Jeremy Frey, Simon Coles, Organizers
Jeremy Frey, Presiding
1:30 pm - 5:00 pm
1:30   Introductory Remarks
1:35 14 Building a semantic chemistry platform with the Royal Society of Chemistry

Valery Tkachenko, tkachenkov@rsc.org, Colin Batchelor, Peter Corbett, Antony Williams.
Abstract - Slides (Slideshare)
2:00 15 Ontology work at the Royal Society of Chemistry

Antony J. Williams, williamsa@rsc.org, Colin Batchelor, Peter Corbett, Jon Steele, Valery Tkachenko.
Abstract - Slides (Slideshare)
2:25 16 PubChem: Data access, navigation, and integration by means of classifiers and ontologies

Evan Bolton, bolton@ncbi.nlm.nih.gov,
Abstract
2:50 17 AMI2: High-through extraction of semantic chemistry from the scientific literature

Andy Howlett, aph36@cam.ac.uk, Mark Williamson, Peter Murray-Rust.
Abstract - Slides (pdf)
3:15   Intermission
3:30 18 Creating context for the experiment record: User-defined metadata

Cerys Willoughby, cerys.willoughby@me.com, Jeremy G Frey, Simon J Coles, Colin L Bird.
Abstract - Slides (pdf) - Poster (pdf)
3:55 19 Experiment markup langauge: A combined markup language and ontology to represent science

Stuart Chalk, schalk@unf.edu,
Abstract - Slides (Slideshare)
4:20 20 Development of formal representations of the synthesis and processing histories of metal-organic frameworks (MOFs) using the ChemAxiom, ChEBI, CMO, and CHEMINF ontologies

Nico Adams1, Nico.Adams@csiro.au, Danielle Kennedy1, Murray Jensen1, Cornelius Kloppers2, Yanfeng Shu2, Claire D'Este2, Craig Lindley2.
Abstract - No slides available
4:45   Panel Discussion

Sunday, March 16, 2014

Translational Cancer Bioinformatics: Data, Methods and Applications - PM Session
Omni Dallas Hotel
Room: Deep Ellum B
Cosponsored by COMP
Rachelle Bienstock, Shuxing Zhang, Organizers
Shuxing Zhang, Presiding
1:00 pm - 3:00 pm
1:00 21 New chemistry and powerful interactive technologies to discover PPI antagonists

Carlos J. Camacho, ccamacho@pitt.edu,
Abstract
1:30 22 Integrative analysis of multidimensional cancer genomics data

Shihua Zhang, Wenyuan Li, Chun-Chi Liu, X. Jasmine Zhou, xjzhouo@usc.edu.
Abstract
2:00 23 New application to estimate the diversity of molecular databases

Iwona Weidlich1, iweidlic@coddes.com, Igor Filippov2.
Abstract - Slides (pdf)
2:30 24 Computational analysis of pleckstrin homology (PH) domains for cancer drug development

Shuxing Zhang, shuxing@gmail.com,
Abstract

Sunday, March 16, 2014

Neglected and Rare Disease Drug Discovery Needs Open Data - PM Session
Omni Dallas Hotel
Room: Deep Ellum B
Antony Williams, Joel Freundlich, Sean Ekins, Organizers
Sean Ekins, Presiding
3:15 pm - 5:15 pm
3:15 25 Looking back at Mycobacterium tuberculosis mouse efficacy testing to move new drugs forward

Sean Ekins1,2, ekinssean@yahoo.com, Robert C Reynolds3, Antony J Williams4, Alex M Clark5, Joel S Freundlich6.
Abstract - Slides (pdf)
3:45 26 Sharing methods to build predictive machine learning models for neglected and rare disease drug discovery

Paul J Kowalczyk, pauljkowalczyk@gmail.com,
Abstract
4:15 27 Royal Society of Chemistry developments to support open drug discovery

Antony J. Williams, williamsa@rsc.org, Alexey Pshenichnov, Jon Steele, Ken Karapetyan, Richard Gay, Valery Tkachenko.
Abstract - Slides (Slideshare)
4:45 28 How can PubChem be leveraged for neglected and rare disease drug discovery?

Evan Bolton, bolton@ncbi.nlm.nih.gov,
Abstract

Sunday, March 16, 2014

CINF Scholarship for Scientific Excellence - EVE Session
Omni Dallas Hotel
Room: Dallas C
Guenter Grethe, Organizers
, Presiding
6:30 pm - 8:30 pm
  29 Efficacy of chemical hyperstructures in similarity searching and virtual screening

Edmund Duesbury, lip12ed@sheffield.ac.uk, John Holliday, Peter Willett.
Abstract
30 3D-QSAR using quantum-mechanics-based molecular interaction fields

Ahmed El Kerdawy1, Ahmed.Elkerdawy@fau.de, Stefan Güssregen2, Hans Matter2, Matthias Hennemann1,3, Timothy Clark1,3,4.
Abstract
31 PoseView: Visualization of protein-ligand interactions in 2D

Katrin Stierand, stierand@zbh.uni-hamburg.de, Matthias Rarey.
Abstract
32 Metal template approach towards efficiency enhancement in hydrogen-bond promoted enantioselective organocatalysis

Tathagata Mukherjee, tathagata.mukherjee@chem.tamu.edu, John A. Gladysz.
Abstract

Monday, March 17, 2014

Keeping the Thrill Alive: Research Data and Electronic Notebooks - AM Session Data Curation
Omni Dallas Hotel
Room: Deep Ellum A
Cosponsored by COMP, MEDI, ORGN, PHYS
Antony Williams, Jeremy Frey, Simon Coles, Leah McEwen, Organizers
Antony Williams, Leah McEwen, Presiding
8:30 am - 11:50 am
8:30   Introductory Remarks
8:35 33 Profiling common types of research data produced by chemists at the University of Michigan

Ye Li, liye@umich.edu,
Abstract - Slides (pdf)
8:55 34 Distributing, managing, and updating cheminformatics experiments

Paul J Kowalczyk, pauljkowalczyk@gmail.com,
Abstract
9:15 35 Dark reaction project: Archiving and deriving value from unreported "failed" hydrothermal synthesis reactions

Joshua Schrier1, jschrier@haverford.edu, Sorelle Friedler2, Alexander Norquist1.
Abstract - No slides available
9:35 36 Factors to consider when choosing the right ELN for capturing and collaborating with your research data

Philip Mounteney1, pm@dotmatics.com, Berkley A Lynch2, Tamsin E Mansley2, Sharang Phatak1, Jess W Sager1.
Abstract
9:55   Intermission
10:10 37 Royal Society of Chemistry activities to develop a data repository for chemistry-specific data

Aileen Day, Alexey Pshenichnov, Ken Karapetyan, Colin Batchelor, Peter Corbett, Jon Steele, Valery Tkachenko, Antony J Williams, williamsa@rsc.org.
Abstract - Slides (Slideshare)
10:30 38 Eureka research workbench: An open source eScience laboratory notebook

Stuart Chalk, schalk@unf.edu,
Abstract - Slides (Slideshare)
10:50 39 PubChem: A platform to archive and share scientific information

Evan Bolton, bolton@ncbi.nlm.nih.gov,
Abstract
11:10 40 Keeping the thrill alive: Data on demand

Berkley A Lynch1, berkley.lynch@dotmatics.com, Tamsin E Mansley1, Philip Mounteney2, Sharang Phatak2, Jess W Sagar2.
Abstract
11:30   Panel Discussion

Monday, March 17, 2014

Keeping the Thrill Alive: Research Data and Electronic Notebooks - PM Session eLab Notebooks
Omni Dallas Hotel
Room: Deep Ellum A
Cosponsored by COMP, MEDI, ORGN, PHYS
Leah McEwen, Antony Williams, Jeremy Frey, Simon Coles, Organizers
Simon Coles, Presiding
1:30 pm - 4:50 pm
1:30   Introductory Remarks
1:35 41 Building a mobile reaction lab notebook

Alex M Clark, aclark@molmatinf.com,
Abstract - Slides (pdf)
1:55 42 Generating metadata for an experiment: Using a tablet ELN

Cerys Willoughby, cerys.willoughby@me.com, Jeremy G Frey, Simon J Coles, Susanne Coles.
Abstract - Slides (pdf) - Poster (pdf)
2:15 43 Mining ELN based structured test and chemical property data to optimize catalyst development

Philip J Skinner, philip.skinner@perkinelmer.com, Joshua A Bishop, Josh.Bishop@PERKINELMER.COM, Rudy Potenzone, Megean Schoenberg.
Abstract - No slides available
2:35 44 Sample management with the LabTrove ELN

Jeremy G Frey, j.g.frey@soton.ac.uk, Simon J Coles, Andrew J Milsted, Cerys Willoughby, Colin L Bird.
Abstract - Slides (pdf)
2:55   Intermission
3:10 45 Digital data repositories in chemistry and their integration with journals and electronic laboratory notebooks

Henry S Rzepa, rzepa@ic.ac.uk, Matt S Harvey, Nick Mason.
Abstract - Slides (html)
3:30 46 Data exchange between electronic lab notebooks and data repositories

Rory Macneil, rmacneil@researchspace.com,
Abstract - Slides (pdf)
3:50 47 Standardized representations of ELN reactions for categorization and duplicate/variation identification

Roger A Sayle, roger@nextmovesoftware.com, Daniel M Lowe.
Abstract - Slides (pdf)
4:10 48 Extracting data, information, and knowledge from an ELN

Colin L Bird1, colinl.bird@soton.ac.uk, Simon J Coles1, Jeremy G Frey1, Richard J Whitby1, Aileen E Day2.
Abstract - Slides (pdf)
4:30   Panel Discussion

Monday, March 17, 2014

Sci-Mix - EVE Session
Dallas Convention Center
Room: Hall F
Jeremy Garritano, Erin Bolstad, Organizers
, Presiding
8:00 pm - 10:00 pm
  2 Ontology-driven information system for chemical and materials science

Nico Adams1, nico.adams@csiro.au, Murray Jensen1, Danielle Kennedy1, Cornelius Kloppers2, Yanfeng Shu2, Claire D'Este2, Craig Lindley2.
Abstract - No slides available
8 Trends in bio-based chemicals: Business intelligence from published literature

Steve M Watson, s.watson@elsevier.com,
Abstract
18 Creating context for the experiment record: User-defined metadata

Cerys Willoughby, cerys.willoughby@me.com, Jeremy G Frey, Simon J Coles, Colin L Bird.
Abstract - Poster (pdf)
20 Development of formal representations of the synthesis and processing histories of metal-organic frameworks (MOFs) using the ChemAxiom, ChEBI, CMO, and CHEMINF ontologies

Nico Adams1, Nico.Adams@csiro.au, Danielle Kennedy1, Murray Jensen1, Cornelius Kloppers2, Yanfeng Shu2, Claire D'Este2, Craig Lindley2.
Abstract
21 New chemistry and powerful interactive technologies to discover PPI antagonists

Carlos J. Camacho, ccamacho@pitt.edu,
Abstract
24 Computational analysis of pleckstrin homology (PH) domains for cancer drug development

Shuxing Zhang, shuxing@gmail.com,
Abstract
26 Sharing methods to build predictive machine learning models for neglected and rare disease drug discovery

Paul J Kowalczyk, pauljkowalczyk@gmail.com,
Abstract
29 Efficacy of chemical hyperstructures in similarity searching and virtual screening

Edmund Duesbury, lip12ed@sheffield.ac.uk, John Holliday, Peter Willett.
Abstract
30 3D-QSAR using quantum-mechanics-based molecular interaction fields

Ahmed El Kerdawy1, Ahmed.Elkerdawy@fau.de, Stefan Güssregen2, Hans Matter2, Matthias Hennemann1,3, Timothy Clark1,3,4.
Abstract
32 Metal template approach towards efficiency enhancement in hydrogen-bond promoted enantioselective organocatalysis

Tathagata Mukherjee, tathagata.mukherjee@chem.tamu.edu, John A. Gladysz.
Abstract
33 Profiling common types of research data produced by chemists at the University of Michigan

Ye Li, liye@umich.edu,
Abstract
34 Distributing, managing, and updating cheminformatics experiments

Paul J Kowalczyk, pauljkowalczyk@gmail.com,
Abstract
35 Dark reaction project: Archiving and deriving value from unreported "failed" hydrothermal synthesis reactions

Joshua Schrier1, jschrier@haverford.edu, Sorelle Friedler2, Alexander Norquist1.
Abstract
36 Factors to consider when choosing the right ELN for capturing and collaborating with your research data

Philip Mounteney1, pm@dotmatics.com, Berkley A Lynch2, Tamsin E Mansley2, Sharang Phatak1, Jess W Sager1.
Abstract
40 Keeping the thrill alive: Data on demand

Berkley A Lynch1, berkley.lynch@dotmatics.com, Tamsin E Mansley1, Philip Mounteney2, Sharang Phatak2, Jess W Sagar2.
Abstract
42 Generating metadata for an experiment: Using a tablet ELN

Cerys Willoughby, cerys.willoughby@me.com, Jeremy G Frey, Simon J Coles, Susanne Coles.
Abstract - Poster (pdf)
46 Data exchange between electronic lab notebooks and data repositories

Rory Macneil, rmacneil@researchspace.com,
Abstract
49 Stepping through virtual communication into Virtmon

Gwendolyn Tennell1,2, gtennell3669@skymail.susla.edu, Feng Li2.
Abstract - Poster (pdf)
63 Your data in the cloud: Facts and fears

Sharang Phatak1, sharang.phatak@dotmatics.com, Berkley A Lynch2, Tamsin E Mansley2, Philip Mounteney1, Jess W Sager1.
Abstract
74 Cheminfomatics for dye chemistry research: Bringing online an unprecedented 100,000 sample dye library

David Hinks1, dhinks@ncsu.edu, Nelson Vinueza-Benitez1, David C Muddiman2, Antony J Williams3.
Abstract

Tuesday, March 18, 2014

Ethical Considerations in Digital Scientific Communication and Publishing - AM Session
Omni Dallas Hotel
Room: Deep Ellum A
Cosponsored by CHAL, CHED, ETHC, PROF, YCC
Leah McEwen, Barbara Moriarty, Edward Mottel, Heather Tierney, Organizers
Heather Tierney, Presiding
8:00 am - 12:00 pm
8:00   Introductory Remarks
8:05 50 Ethical dilemmas in the creation and sharing of a crystallographic database system

Suzanna Ward, ward@ccdc.cam.ac.uk, Colin R Groom.
Abstract - Slides (pdf)
8:30 51 Image manipulation in scholarly publishing: Setting standards and promoting best practice

Christina Bennett, cbennett@the-aps.org,
Abstract - No slides available
8:55 52 Tools for identifying potential misconduct: The CrossCheck service from CrossRef

Rachael Lammey, rlammey@crossref.org,
Abstract - Slides (pdf)
9:20 53 Mapping the terrain of publication ethics

Charon A Pierson, cpierson@aanp.org,
Abstract - Slides (pdf)
9:45   Intermission
9:55 54 Publication ethics in ACS journals: Education and verification

Anne Coghill, a_coghill@acs.org,
Abstract
10:20 55 Ethics in scientific publication: Observations of an editor and recommended best practices for authors

Kirk S Schanze, kschanze@chem.ufl.edu,
Abstract
10:45 56 Dealing with scientific misconduct: Part of an editor's day-to-day work

Haymo Ross, hross@wiley.com,
Abstract - No slides available
11:10 57 Role of the journal editor in maintaining ethical standards in the changing publishing environment

Jamie Humphrey, ruthvens@rsc.org, Sarah Ruthven.
Abstract
11:35   Panel Discussion moderated by Gregory Ferrence

Tuesday, March 18, 2014

Cloud Computing in Cheminformatics - PM Session
Omni Dallas Hotel
Room: Deep Ellum A
Cosponsored by COMP
Rudolph Potenzone, Organizers
Rudolph Potenzone, Presiding
1:40 pm - 5:30 pm
1:40   Introductory Remarks
1:45 58 10 Years of collaborative drug discovery in the cloud

Barry A. Bunin, bbunin@collaborativedrug.com,
Abstract - Slides (pdf)
2:15 59 Cloud-hosted APIs for cheminformatics designed for real time user interfaces

Alex M Clark, aclark@molmatinf.com,
Abstract - Slides (pdf)
2:45 pm 60 WITHDRAWN
3:15   Intermission
3:30 61 Application of cloud computing to Royal Society of Chemistry data platforms

Valery Tkachenko, tkachenkov@rsc.org, Ken Karapetyan, Jon Steele, Alexey Pshenichnov, Antony J. Williams.
Abstract - Slides (Slideshare)
4:00 62 PubChem in the cloud

Paul Thiessen, Bo Yu, Gang Fu, Evan Bolton, bolton@ncbi.nlm.nih.gov.
Abstract
4:30 63 Your data in the cloud: Facts and fears

Sharang Phatak1, sharang.phatak@dotmatics.com, Berkley A Lynch2, Tamsin E Mansley2, Philip Mounteney1, Jess W Sager1.
Abstract
5:00 64 Moving main stream chemical research to the cloud

Philip J. Skinner, Philip.skinner@perkinelmer.com, Joshua Bishop, Phil McHale, Rudy Potenzone.
Abstract

Wednesday, March 19, 2014

New Models in Substance Discovery - AM Session
Omni Dallas Hotel
Room: Deep Ellum A
Roger Schenck, Organizers
Roger Schenck, Presiding
8:10 am - 12:00 pm
8:10   Introductory Remarks
8:15 65 Functional requirements for chemical information retrieval for intellectual property professionals

Matthew McBride, mmcbride@cas.org,
Abstract
8:45 66 New approaches to search interfaces in PubChem

Asta Gindulyte, Lianyi Han, Paul Thiessen, Bo Yu, Lewis Geer, Evan Bolton, bolton@ncbi.nlm.nih.gov.
Abstract
9:15 67 From searching to finding: New developments for managing large data sets

Juergen Swienty-Busch1, j.swienty-busch@elsevier.com, David Evans2.
Abstract
9:45 68 Search and navigation functionality for a major reference work online: SOS 4.0

Fiona Shortt de Hernandez1, fiona.shortt@thieme.de, Guido F. Herrmann1, Peter Loew2.
Abstract
10:15   Intermission
10:30 69 Chemical most common denominator: Use of chemical structures for semantic enrichment and interlinking of scientific information

Valentina Eigner-Pitto, ve@infochem.de, Josef Eiblmaier, Hans Kraut, Larisa Isenko, Heinz Saller, Peter Loew.
Abstract - Slides (pdf)
11:00 70 Representation and display of non-standard peptides using semi-systematic amino acid monomer naming

Roger A Sayle, roger@nextmovesoftware.com, Noel M O'Boyle.
Abstract - Slides (pdf)
11:30 71 New structure search capabilities for accessing CAS content

Kurt Zielenbach1, kzielenbach@cas.org, Bryan Harkleroad2.
Abstract

Wednesday, March 19, 2014

General Papers - PM Session
Omni Dallas Hotel
Room: Deep Ellum A
Jeremy Garritano, Erin Bolstad, Organizers
Erin Bolstad, Presiding
1:30 pm - 3:30 pm
1:30 72 UK National Chemical Database Service: An integration of commercial and public chemistry services to support chemists in the United Kingdom

Antony J. Williams, williamsa@rsc.org, Valery Tkachenko, Richard Kidd.
Abstract - Slides (Slideshare)
2:00 73 Data enhancing the Royal Society of Chemistry publication archive

Antony J. Williams, williamsa@rsc.org, Colin Batchelor, Peter Corbett, Ken Karapetyan, Valery Tkachenko.
Abstract - Slides (Slideshare)
2:30 74 Cheminfomatics for dye chemistry research: Bringing online an unprecedented 100,000 sample dye library

David Hinks1, dhinks@ncsu.edu, Nelson Vinueza-Benitez1, David C Muddiman2, Antony J Williams3.
Abstract - Slides (pdf)
3:00 75 QM/MM docking for GPCR targets

Art E Cho, artcho@korea.ac.kr, Minsup Kim.
Abstract - Slides (pdf)

CHED, Christine Jaworek-Lopes, Irvin Levy, Beatriz Rios-McKee Wednesday, March 19, 2014

Mobile Devices, Augmented Reality, and The Mobile Chemistry Classroom - AM Session
Hyatt Regency Dallas
Room: Gaston A/B
Cosponsored by CINF
Antony Williams, Harry Pence, Organizers
Antony Williams, Harry Pence, Presiding
8:30 am - 10:55 am
8:30   Introductory Remarks
8:35 1552 How will mobile devices change the traditional classroom?
Harry E. Pence
8:55 1553 Effect of iPad Minis and iSpartan on student performance in a one-semester organic chemistry course
Jacqueline Bennett, Maurice O. Odago.
9:15 1554 Student reponse to an iPad-saturated General Chemistry classroom and laboratory
Cynthia Powell
9:35   Intermission
9:50 1555 Teaching molecular symmetry using mobile devices
Dean H Johnston
10:10 1556 Flipped classroom tech: What it looks like and how it compares to tech in a traditional classroom
Lucille A Benedict, Julie Ziffer.
10:30 1557 Independent learning of organic chemistry concepts through electronic scaffolding: Nomenclature through online videos accompanied by tailored worksheets
Issam Kobrsi
10:50   Concluding Remarks

CHED, Christine Jaworek-Lopes, Irvin Levy, Beatriz Rios-McKee Wednesday, March 19, 2014

Mobile Devices, Augmented Reality, and The Mobile Chemistry Classroom - PM Session
Hyatt Regency Dallas
Room: Gaston A/B
Cosponsored by CINF
Harry Pence, Organizers
Antony Williams, Harry Pence, Presiding
1:30 pm - 3:35 pm
1:30   Introductory Remarks
1:35 1591 Chemistry 151 and 152: Why yes, "There is a Wayne Community College General Chemistry App for That"
Ashton T. Griffin
1:55 1592 Teaching complex concepts with simple mobile apps
Lisa B. Lewis, Ian F. MacInnes, Alex M. Clark.
2:15 1593 Evaluation and testing of Smartphone CSI applications for forensic science courses
Kelly M. Elkins, Zoe Krohn.
2:35   Intermission
2:50 1594 Taking advantage of the many functions and features of clickers to engage students in general chemistry courses
Derek A Behmke
3:10 1595 Accessing Royal Society of Chemistry resources and making chemistry mobile
Antony J Williams, Alexey Pschenichnov, Valery Tkachenko.
3:30   Concluding Remarks

COMP, Emilio Esposito, Scott Wildman Tuesday, March 18, 2014

ACS Award for Computers in Chemical and Pharmaceutical Research: Symposium in Honor of Martin Stahl - AM Session
Omni Dallas Hotel
Room: Trinity 6
Cosponsored by BIOL, CINF, MEDI, PHYS
Emilio Esposito, Martin Stahl, Terry Stouch, Organizers
Martin Stahl, Presiding
8:30 am - 11:20 am
8:30   Introductory Remarks
8:35 108 Molecular recognition and structure-based design
Francois N. Diederich
9:05 109 Influence of water molecules on protein-ligand binding: Correlation of structure and thermodynamic signature
Stefan G. Krimmer, Adam Biela, Michael Betz, Andreas Heine, Gerhard Klebe.
9:35 110 Ligand design incorporating network concepts and binding site flexibility
Neil R Taylor, Bernd Kuhn.
10:05   Intermission
10:20 111 Predicting protein conformational response in ligand discovery
Marcus Fischer, Ryan G. Coleman, James S. Fraser, Brian K. Shoichet.
10:50 112 Evolving role of modeling and informatics in drug discovery
W. Patrick Walters

COMP, Emilio Esposito, Scott Wildman Tuesday, March 18, 2014

ACS Award for Computers in Chemical and Pharmaceutical Research: Symposium in Honor of Martin Stahl - PM Session
Omni Dallas Hotel
Room: Trinity 6
Cosponsored by BIOL, CINF, MEDI, PHYS
Emilio Esposito, Martin Stahl, Terry Stouch, Organizers
Terry Stouch, Presiding
1:30 pm - 4:50 pm
1:30   Introductory Remarks
1:35 132 Drug discovery and development by design: Using the knowledge from every organic crystal structure ever published
Colin R Groom, Neil Feeder, Elna Pidcock, Peter A Wood, Peter TA Galek.
2:05 133 Biophysical dominos: Protein ensembles from room temperature X-ray crystallography
James S Fraser
2:35 134 Application of extended Hueckel theory to molecular interactions and conformations
Paul Labute, Christopher Williams.
3:05   Intermission
3:20 135 Modeling with experimental data at your fingertips
Matthias Rarey
3:50 136 Complementarity between empirical and computational fragment screens
Sarah Barelier, Oliv Eidam, Inbar Fish, Johan Hollander, Francis Figaroa, Ruta Nachane, John Irwin, Brian Shoichet, Gregg Siegal.
4:20 137 Award Address (ACS Award for Computers in Chemical and Pharmaceutical Research sponsored by the ACS Division of Computers in Chemistry). Adventures in molecular design: A trip report
Martin Stahl

COMP, Emilio Esposito, Scott Wildman Wednesday, March 19, 2014

Computational Approaches To Spectroscopy Analysis - PM Session Sorry To Keep You Waiting #ACSdallas. Enjoy!
Omni Dallas Hotel
Room: Trinity 7
Cosponsored by ANYL, CINF, PHYS
Emilio Esposito, Y. Jane Tseng, Organizers
Symon Gathiaka, Presiding
1:00 pm - 5:15 pm
1:00 316 Ab initio molecular dynamics study of non aqueous fluids: Cases of ammonia and methanol in ambient and supercritical conditions
Vivek Kumar Yadav
1:30 317 What does the precision of NMR-derived protein structures tell us? Considering the impact of NMR in studying protein chemistry
David A Snyder, Anthony Riga, Saadia Chaudhry.
2:00 318 Modeling fluorescence observables, particularly for FRET experiments, using Markov chain analysis of molecular dynamics simulations
Brent P Krueger, Amy L Speelman, Katie L Hinkle, Darren B VanBeek.
2:30 319 Batch normalizer, a fast total abundance regression calibration method to simultaneously adjust batch and injection order effects in liquid chromatography/time-of-flight mass spectrometry-based metabolomics data and comparison with current calibration methods
San-Yuan Wang, Ching-Hua Kuo, Yufeng J Tseng.
3:00   Intermission
3:15 320 Polyelectrolyte wants a surface: Modeling vibrational sum-frequency spectra of polyelectrolytes at oil-water interfaces
Nicholas A Valley, Geraldine L Richmond.
3:45 321 Search prefilters for infrared library searching in the PDQ database to enhance investigative lead information from automotive paints
Barry K Lavine, Ayuba Fasasi, Collin White, Razvan Ionut Stoian, Mark Sandercock.
4:15 322 Through the looking glass: Watching atomic dynamics with neutrons and numbers with VISION
Anibal J Ramirez-Cuesta, Sihai Yang, Martin Schröder.
4:45 323 Theoretical formulation and computational simulation of electronic sum-frequency generation (ESFG) spectroscopy of surfactant on water surface
Chih-Kai Lin, Michitoshi Hayashi, Sheng Hsien Lin.

COMP, Emilio Esposito, Scott Wildman Sunday, March 16, 2014

Computational Study of Water - AM Session Models, Behaviors and Exploitations: No Waters were Hurt in this Research
Omni Dallas Hotel
Room: Trinity 5
Cosponsored by BIOL, CINF, MEDI, PHYS
Daniel Sindhikara, Organizers
Jiaqi Wang, Presiding
8:30 am - 11:45 am
8:30 13 Reorganization of water in redox reactions
Murat Kilic, Bernd Ensing.
9:00 14 How well can the properties of liquid water be described without the inclusion of many-body exchange forces?
Omololu Akin-Ojo, Krzysztof Szalewicz.
9:30 15 Water potential from first principles
Volodymyr Babin, Francesco Paesani.
10:00   Intermission
10:15 16 Exploring thermodynamics over water model parameter space
Michael R Shirts, Himanshu Paliwal.
10:45 17 Real hydrophobic effect: Applications to target assessment, lead optimization, and binding selectivity
Woody Sherman
11:15 18 Using a water interaction model for developing protein-ligand scoring functions
Nadine Schneider, Gudrun Lange, Sally Hindle, Robert Klein, Matthias Rarey.

COMP, Emilio Esposito, Scott Wildman Sunday, March 16, 2014

Drug Discovery - AM Session Information Equal Power #fightTheFuture #drugDisco #informatics
Omni Dallas Hotel
Room: Trinity 6
Cosponsored by BIOL, CINF, MEDI, PHYS
Scott Wildman, Y. Jane Tseng, Organizers
Luke Achenie, Presiding
8:30 am - 11:45 am
8:30 7 Novel applications of SAR matrices in pharmaceutical research
Liying Zhang, Jeremy Starr, Dilyana Dimova, Preeti Iyer, Disha Gupta-Ostermann, Antonio de la Vega de Leon, Jürgen Bajorath, Veerabahu Shanmugasundaram.
9:00 8 SMARTSeditor: A graphical approach to the creation of chemical patterns
Karen Schomburg, Katrin Stierand, Lars Wetzer, David Seier, Stefan Bietz, Matthias Rarey.
9:30 9 Increasing the 3D character of PPI screening libraries via intuitive substructure matches
Christian Laggner
10:00   Intermission
10:15 10 Accessorize your drugs: Adaptive combinatorial design of multi-target profiles
Gisbert Schneider, Michael Reutlinger, Tiago Rodrigues, Petra Schneider.
10:45 11 Advances in multiparameter optimisation: Targeting the "best" profile for your project's objectives
Matthew Segall, Iskander Yusof, Ed Champness.
11:15 12 Right metrics at the right time and for the right questions – drug design strategies from virtual screening to optimization and selection of drug-candidates
Johan Ulander, Fredrik Bergström, Ulf Bredberg, Thomas Drmota, Öjvind Davidsson, Jörgen Jensen, Malin Lemurell, Antonio Llinas, Carl-Gustav Sigfridsson, Carl Whatling, Susanne Winiwarter.

COMP, Emilio Esposito, Scott Wildman Sunday, March 16, 2014

Drug Discovery - PM Session First #methodMadness Session of #ACSdallas! #loveit #goodStart #greatAfternoon
Omni Dallas Hotel
Room: Trinity 6
Cosponsored by BIOL, CINF, MEDI, PHYS
Scott Wildman, Y. Jane Tseng, Organizers
Edward Sherer, Presiding
1:30 pm - 5:15 pm
1:30 31 Analysis of prototropic and ring-chain tautomerism to predict favorable tautomers in drug-like molecules
Laura Guasch, Marc C. Nicklaus.
2:00 32 Prediction of tautomers and protonation states in protein-ligand binding sites
Stefan Bietz, Sascha Urbaczek, Matthias Rarey.
2:30 33 Structurally conserved binding sites of hemagglutinin revisited by ProBiS
Dusanka Janezic
3:00 34 Enhanced Monte Carlo sampling through replica exchange with solute tempering (REST)
Daniel J Cole, Julian Tirado-Rives, William L Jorgensen.
3:30   Intermission
3:45 35 Combining QSAR-analysis and fragment-based drug design in search for new anti-HIV agents
Olga A. Tarasova, Alexandra F. Urusova, Alexey V. Zakharov, Dmitry A. Filimonov, Vladimir V. Poroikov.
4:15 36 Conformational flexibility in drug design of anti-apoptotic proteins inhibitors
Claire Colas, Sandy Desrat, Vincent Dumontet, Nicolas Birlirakis, Fanny Roussi, Bogdan I Iorga.
4:45 37 Entropic keys to the histone code
Bradley Dickson, Dmitri Kireev.

COMP, Emilio Esposito, Scott Wildman Monday, March 17, 2014

Drug Discovery - AM Session Ligand-Based Design is King! #biased #QSARguru #drugDisco
Omni Dallas Hotel
Room: Trinity 6
Cosponsored by BIOL, CINF, MEDI, PHYS
Scott Wildman, Y. Jane Tseng, Organizers
Hector Gonzalez, Presiding
8:30 am - 11:45 am
8:30 58 Predictive application of bioisostere transformations to identify novel high quality compound ideas
Ed Champness, Julian Hayward, John Barnard, James Chisholm, Chris Leeding, Matthew Segall.
9:00 59 Computational analyses of RNA repeat expansions causing genetic disease
Ilyas Yildirim, HaJeung Park, Jessica L Childs-Disney, Matthew D Disney, George C Schatz.
9:30 60 Elucidation of binding of novel Skp2-SCF complex inhibitors through pharmacophore modeling and molecular dynamics simulations
John K Morrow
10:00   Intermission
10:15 61 Computational insights into the alkylation reactions of pyridine and pyridinium quinone methide precursors: Studies towards the re-alkylation of aged actetylcholinesterase
Andrew J Franjesevic, Keegan Fitzpatrick, Jason Brown, Ryan Yoder, Jeremey Beck, Christopher S Callam, Christopher M Hadad.
10:45 62 Importance of tetrahydrobiopterin mediated interactions in aromatic amino acid hydroxylases enzymes family: Assessing effect on biosynthesis due to effect of single site mutation on thermodynamic stability of hydroxylases
Nidhi Chadha, Anjani Kumar Tiwari, Shubhra Chaturvedi, Marilyn Daisy Milton, Anil Kumar Mishra.
11:15 63 Examining binding and reaction mechanisms of hydroxyurea as a biological nitric oxide donor using QM/MM reaction path methods
Sai L Vankayala, Jacqueline C Hargis, Fiona Kearns, Henry L Woodcock.

COMP, Emilio Esposito, Scott Wildman Monday, March 17, 2014

Drug Discovery - PM Session A Little #methodMadness Never Hurts: See You Here!
Omni Dallas Hotel
Room: Trinity 6
Cosponsored by BIOL, CINF, MEDI, PHYS
Scott Wildman, Y. Jane Tseng, Organizers
Melissa Landon, Presiding
1:30 pm - 5:15 pm
1:30 81 Leveraging data fusion strategies in multi-receptor lead optimization MM/GBSA end-point methods
Jennifer L Knight, Goran Krilov, Robert Abel.
2:00 82 Evaluation of free energy perturbation methods in drug discovery: Lessons learned and recommendations
Elizabeth S Parks, Ray J Unwalla, Rajiah Aldrin Denny.
2:30 83 Measuring the conformational free energy of binding: Can it be high or are there other explanations?
Gregory L Warren, Matthew T Geballe, Paul C. D. Hawkins, Hideyuki Sato, Gunther Stahl, Christopher I Bayly.
3:00 84 Exploring the drug binding ensemble using Hamiltonian replica exchange simulations
Michael R Shirts, Kai Wang, John D Chodera.
3:30   Intermission
3:45 85 FFT-based fragment-based drug design on a set of drug targets
David R Hall, Dmitri Beglov, Dima Kozakov, Sandor Vajda.
4:15 86 Support vector machine (SVM) and pharmacophore-based models for selecting, optimizing, and prioritizing anthrax toxin lethal factor (LF) inhibitors
Elizabeth A Amin, Ting-Lan Chiu, Xia Zhang.
4:45 87 Strategies for lead discovery using footprint similarity scoring
Robert C Rizzo

COMP, Emilio Esposito, Scott Wildman Wednesday, March 19, 2014

Drug Discovery - AM Session Want a Challenge? Try ADME/Tox #drugDisco
Omni Dallas Hotel
Room: Trinity 6
Cosponsored by BIOL, CINF, MEDI, PHYS, TOXI
Scott Wildman, Y. Jane Tseng, Organizers
George Patargias, Presiding
8:30 am - 11:15 am
8:30 300 Addressing toxicity risk when designing and selecting compounds in early drug discovery
Matthew Segall, Chris Barber.
9:00 301 Training cytochrome P450 site of metabolism models with region-level data
S. Joshua Swamidass, Jed Zaretzki, Michael Browning.
9:30 302 New tool for drug design and ADMET studies: Multiprotic pKa model with significantly improved prediction accuracy and vastly expanded applicability domain
Robert Fraczkiewicz, Mario Lobell, Robert D. Clark, Alexander Hillisch, Andreas H. Göller, Ursula Krenz, Rolf Schoenneis.
10:00   Intermission
10:15 303 Using open source tools and public data to build machine learning models in support of ADMET in silico modeling
Paul J Kowalczyk
10:45 304 QSAR modelling of rodent acute toxicity
Alexey V. Zakharov, Marc C. Nicklaus.

COMP, Emilio Esposito, Scott Wildman Wednesday, March 19, 2014

Drug Discovery - PM Session Structural Bioinformatics and Target-Based #drugDisco #informationIsPower
Omni Dallas Hotel
Room: Trinity 6
Cosponsored by BIOL, CINF, MEDI, PHYS
Scott Wildman, Y. Jane Tseng, Organizers
Lingling Jiang, Presiding
1:00 pm - 5:15 pm
1:00 324 Fractal dimensions of ligand-binding sites: A fresh view on macromolecular structure
Gisbert Schneider, Nickolay Todoroff, Gerhard Hessler, Karl-Heinz Baringhaus.
1:30 325 Enhancing B-cell epitope predictions by integrating protein sequence and structural bioinformatics
Steven J Darnell, Martin Riese, Erik G Edlunde, Frederick R Blattner.
2:00 326 Discovery of novel inhibitors targeting GAB1 pleckstrin homology domain
Lu Chen, Lei Du-Cuny, Sylvestor Moses, Sabrina Dumas, Zuohe Song, Emmanuelle J Meuillet, Shuxing Zhang.
2:30 327 Dynamics guided inhibitor design for Ras
Alemayehu A Gorfe
3:00   Intermission
3:15 328 Computational mapping improves selection of the bound ligand pose from the set of docking poses
Dmitri Beglov, David R Hall, Dima Kozakov, Sandor Vajda.
3:45 329 FTFlex: Incorporating protein side chain flexibility into computational protein mapping
Laurie E. Grove, Idriss Slaoui, David R. Hall, Dmitri Beglov, Dima Kozakov, Sandor Vajda.
4:15 330 Implementation and evaluation of a multi-grid scoring function for structure-based design
William J Allen, Trent E Balius, Sudipto Mukherjee, Robert C Rizzo.
4:45 331 Mechanistic and inhibition studies of the Arp2/3 complex, a key regulator of the actin cytoskeleton
George Patargias, Plato A Magriotis, Maria Panagiotou, Byron Hetrick, Julianna Han, Mike Montgomery, Andrew Baggett, Min S Han, Adam C Glass, Shih Y Liu, Brad J Nolen, Zoe Cournia.

COMP, Emilio Esposito, Scott Wildman Tuesday, March 18, 2014

Material Science - AM Session A True Example
Omni Dallas Hotel
Room: Trinity 5
Cosponsored by CINF, COLL, PHYS, PMSE, POLY
Maciej Haranczyk, Organizers
Hedieh Torabifard, Presiding
8:30 am - 11:45 am
8:30 113 Using surface adsorption and entropic barriers to improve gas separation by 2D nanoporous membranes
Joshua Schrier
9:00 114 Revised basin-hopping Monte Carlo algorithm for structure optimization of clusters and nanoparticles
Gustavo G. Rondina, Juarez L. F. Da Silva.
9:30 115 Oxygen adsorption characteristics on hybrid carbon and boron-nitride nanotubes
Haining Liu, C Heath Turner.
10:00   Intermission
10:15 116 Parametric study of PEO based thermoplastic polyurethane silica nanocomposites
Oguzhan Oguz, Kaan Bilge, Ozge Malay, Melih Papila, Iskender Yilgor, Yusuf Ziya Menceloglu.
10:45 117 Energetic investigations of the r-BN to c-BN transformation via first-principles and classical molecular dynamics modeling
Christin P Morrow, Prajay Patel, Peter Kroll.
11:15 am 118 WITHDRAWN

COMP, Emilio Esposito, Scott Wildman Tuesday, March 18, 2014

Material Science - PM Session Chemistry in Action! #matScience #coolStuff
Omni Dallas Hotel
Room: Trinity 7
Cosponsored by CINF, COLL, PHYS, PMSE, POLY
Maciej Haranczyk, Organizers
Hector Velazquez, Presiding
1:30 pm - 5:15 pm
1:30 125 Modeling and simulation of hydrogen diffusion and reaction in semiconductor photonic materials
Isaac S. Lavine, Joshua A. Levinson, Kenneth G. Glogovsky.
2:00 126 Electron transport across a metal-organic interface
Kurt Stokbro
2:30 127 What chemistries will bring low hole effective mass transparent conducting oxides? A high-throughput computational analysis
Geoffroy Hautier, Anna Miglio, Gerbrand Ceder, Gian-Marco Rignanese, Xavier Gonze.
3:00 128 Atomistic simulations of extended defects in oxide energy materials
Stephen C Parker, Stephen R Yeandel, Marco Molinari.
3:30   Intermission
3:45 129 High-throughput quantum chemistry and virtual screening for organic semiconductor solutions
Mathew D Halls, David J Giesen, H. Shaun Kwak, Alexander Goldberg, Thomas F Hughes, Yixiang Cao, Jacob L Gavartin.
4:15 130 Predictions of charge transfer in organic photovoltaic materials
Alexander Goldberg, Mathew D Halls, Yixing Cao, David Giesen, Thomas Hughes, Shaun Qwak.
4:45 131 First principles modeling of organic energy materials: Development of efficient methodologies, rationales, and applications
Daniel S Lambrecht, Keith A Werling, Maryanne Griffin, Geoffrey R Hutchison.

COMP, Emilio Esposito, Scott Wildman Wednesday, March 19, 2014

Material Science - AM Session Atomistic Exploration of Materials #matScience
Omni Dallas Hotel
Room: Trinity 5
Cosponsored by CINF, COLL, PHYS, PMSE, POLY
Maciej Haranczyk, Organizers
Caley Allen, Presiding
8:30 am - 11:15 am
8:30 305 First-principles studies of amorphous silicon oxycarbide: Correlating structural properties with 29Si-NMR chemical shifts
John P Nimmo, Peter Kroll.
9:00 306 First principles prediction on the formation and properties of polyanion deficient iron phosphate
Yu-Hao Tsai, Gyeong S. Hwang.
9:30 307 Structure and thermochemistry of Hafnium-silicate glasses
Atreyi Dasmahapatra, Peter Kroll.
10:00   Intermission
10:15 308 Li insertion in SiCO ceramics
Tran T Tran, Peter Kroll.
10:45 309 Electronic structures and optical properties of silver nanoparticles studied by TDDFT magnetic circular dichroism spectra
Natalia Karimova, Christine M. Aikens.

COMP, Emilio Esposito, Scott Wildman Monday, March 17, 2014

Membranes - AM Session The Incredible Membrane #sometimesEdible #insaneAsAlways
Omni Dallas Hotel
Room: Trinity 5
Cosponsored by BIOL, CINF, COLL, MEDI, PHYS, PMSE, POLY
Michael Feig, Organizers
Kellon Belfon, Presiding
8:30 am - 11:15 am
8:30 64 Electrostatics-driven shape transitions in charged elastic membranes
Vikram Jadhao, Creighton K. Thomas, Monica Olvera de la Cruz.
9:00 65 Structure and phase behavior of Langmuir monolayers at the air/water interface
Wei Lin, Francesco Paesani.
9:30 66 Multiscale modeling of paclitaxel interacting with cellular membranes
Myungshim Kang, Sharon Loverde.
10:00   Intermission
10:15 67 Molecular basis of action of the AT1 antagonist losartan
Maria Zervou, Zoe Cournia, Constantinos Potamitis, George Patargias, Serdar Durdagi, Simona Golic Grdadolnik, Thomas Mavromoustakos.
10:45 68 Ras proteins membrane dynamics and lateral organization
Alemayehu A Gorfe

COMP, Emilio Esposito, Scott Wildman Sunday, March 16, 2014

Molecular Mechanics - PM Session These Talks Will be Polarizing: You've Been Warned (Electrostatics and Polarization)
Omni Dallas Hotel
Room: Trinity 5
Cosponsored by BIOL, CINF, MEDI, PHYS
Michael Feig, Organizers
Nathan Deyonker, Presiding
1:30 pm - 5:15 pm
1:30 38 Many-body expansions for the dipole moment of water: Toward first principles modeling of vibrational spectroscopies
Gregory R. Medders, Francesco Paesani.
2:00 39 Applying the fluctuation-dissipation theorem to compute local dielectric properties
David M Rogers
2:30 40 Charge transfer and polarizability in the KcsA potassium channel via molecular mechanics
Marielle Soniat, Susan B. Rempe, Steven W. Rick.
3:00 pm 41 WITHDRAWN
3:30   Intermission
3:45 42 Reactivity of chloroperoxidase, a promising bioengineering target, revealed through simulation
David C Chatfield, Armando D Pardillo, Rui Zhang, Xiaotang Wang, Cassian D'Cunha, Alexander N Morozov.
4:15 43 Charge transfer in polarizable force fields: Importance of the electronic kinetic energy
Toon Verstraelen, Paul W Ayers, Veronique Van Speybroeck, Michel Waroquier.
4:45 44 Fast and accurate generation of ab initio quality atomic charges using nonparametric statistical regression
Brajesh K Rai, Gregory A Bakken.

COMP, Emilio Esposito, Scott Wildman Monday, March 17, 2014

Molecular Mechanics - PM Session Applying Sanity to the #methodMadness We're Talking Applications #molMech
Omni Dallas Hotel
Room: Trinity 5
Cosponsored by BIOL, CINF, MEDI, PHYS
Michael Feig, Organizers
William Allen, Presiding
1:30 pm - 5:15 pm
1:30 88 Novel approach for high throughput gas separation screenings of commonly utilized zeolites
Keith V Lawler, Paul M Forster.
2:00 89 Theoretical simulations of n-alkane unimolecular cracking on zeolites
Bess Vlaisavljevich, Amber Janda, Alexis T Bell, Berend Smit.
2:30 90 Mechanism and dynamics of encapsulation in molecular apple peels
Ara M. Abramyan, Zhiwei Liu, Vojislava Pophristic.
3:00 91 Calculation of surface tensions for model crude oils with water
Nandhini Sokkalingam, Joshua Deetz, Varuni Dantanarayana, Koichi Takamura, Roland Faller.
3:30   Intermission
3:45 92 Triplet and quadruplet particle correlations in liquids and liquid mixtures from simulation and experiment
Elizabeth A. Ploetz, Sadish Karunaweera, Paul E. Smith.
4:15 93 Conformational flexibility of cyclic imine phycotoxins revealed by long-timescale molecular dynamics simulations
Rómulo Aráoz, Evelyne Benoit, Jordi Molgó, Bogdan I Iorga.
4:45 94 Potential anticancer agent, Laulimalide, binding to tubulin protofilaments
Cassandra D.M. Churchill, Mariusz Klobukowski, Jack A. Tuszynksi.

COMP, Emilio Esposito, Scott Wildman Tuesday, March 18, 2014

Molecular Mechanics - PM Session Nature's Functional Polymers: Yeah, I Said It, What You Going To Do @acsPOLY?
Omni Dallas Hotel
Room: Trinity 5
Cosponsored by BIOL, CINF, MEDI, PHYS, POLY
Michael Feig, Organizers
Brent Krueger, Presiding
1:30 pm - 5:15 pm
1:30 138 Conformation-directed catalysis and coupled enzyme-substrate dynamics in the phosphorylation dependent cis-trans isomerase Pin1
Hector Adam Velazquez, Donald Hamelberg.
2:00 139 Towards a better understanding of enzyme catalyis through the mean reaction force: The case study of Pin1
Esteban Vöhringer-Martinez
2:30 140 Modulation of active site electronic structure by the protein matrix to control [NiFe] hydrogenase reactivity
Dayle M Smith, Simone Raugei, Thomas C. Squier.
3:00 141 Structure and dynamics analysis on plexin-B1 Rho GTPase binding domain monomer and dimer
Liqun Zhang, Matthias Buck.
3:30   Intermission
3:45 142 Ion binding preference in ribosomal GTPase associated center (GAC)
Hamed S. Hayatshahi, Thomas E. Cheatham III.
4:15 143 Heterogeneous preferential solvation of water and trifluoroethanol in homologous lysozyme systems
Evan J Arthur, John T King, Kevin J Kubarych, Charles L Brooks.
4:45 144 Beta-hairpin prone region in alpha-synuclein monomer: A possible site to initiate oligomerization revealed by extensive molecular dynamics simulations
Hang Yu, Wei Han, Klaus Schulten.

COMP, Emilio Esposito, Scott Wildman Wednesday, March 19, 2014

Molecular Mechanics - AM Session Dropping Knowledge on Force Fields. Too Bad this Session isn't on #mayTheFourth
Omni Dallas Hotel
Room: Trinity 7
Cosponsored by BIOL, CINF, MEDI, PHYS
Michael Feig, Organizers
Brian Fochtman, Presiding
9:00 am - 11:45 am
9:00 295 Towards accurate parameterization of imidazolium based ionic liquid potentials
Hedieh Torabifard, Oleg N Starovoytov, G. Andres Cisneros.
9:30 296 Development of realistic molecular models for aqueous electrolyte solutions
Lukas Vlcek, Ariel A Chialvo, John M Simonson.
10:00 297 Arylamide foldamers: From force field development to applications
Vojislava Pophristic, Zhiwei Liu, Ara Abramyan, Marianne Wujcik, Jhenny Galan, Jessica Geer, Eduardo Sproviero, Guillermo Moyna.
10:30   Intermission
10:45 298 Development and test of the second generation of the general AMBER force field
Junmei Wang
11:15 299 MARTINI model for deducing mechanical properties of cellulose fibrils
Cesar A Lopez Bautista, Giovanni Bellesia, Paul Langan, Siewert Jan Marrink, S. Gnanakaran.

COMP, Emilio Esposito, Scott Wildman Wednesday, March 19, 2014

Molecular Mechanics - PM Session Sorry it Took us so Long To Get To #molMech #methodMadness March is Just Full of Madness. #hoops
Omni Dallas Hotel
Room: Trinity 5
Cosponsored by BIOL, CINF, MEDI, PHYS
Michael Feig, Organizers
Y. Jane Tseng, Presiding
1:00 pm - 4:45 pm
1:00 332 Advances in reservoir replica exchange methodology
Benjamin T Miller, Ana Damjanovic, Daniel B Smith, Bernard R Brooks.
1:30 333 Extending atomistic simulation timescale in solid/liquid systems: Crystal growth from solution by a parallel-replica dynamics and continuum hybrid method
Chun-Yaung Lu, Arthur F. Voter, Danny Perez.
2:00 334 On-the-path random walk sampling to enable multi-step-multi-coordinate enzyme reaction simulations
Wei Yang
2:30 335 Sampling the energy landscape of proteins and protein aggregates
Ulrich H.E. Hansmann
3:00   Intermission
3:15 336 Efficient property prediction using visited states simulations over many thermodynamic states
Michael R Shirts, Arjan C Kool, Jacob I Monroe.
3:45 337 Linear basis function approach to efficent alchemical free energy calculations
Levi N Naden, Michael R. Shirts.
4:15 338 First tests of a hybrid quantum-chemical approach for free energy calculations
Gerhard König, Frank C Pickard, Ye Mei, Bernard R Brooks.

COMP, Emilio Esposito, Scott Wildman Tuesday, March 18, 2014

Poster Session - EVE Session
Dallas Convention Center
Room: Hall E
Cosponsored by BIOL, CINF, COLL, ENFL, ENVR, FLUO, GEOC, HIST, I&EC, INOR, MEDI, ORGN, PHYS, PMSE, POLY, TOXI, YCC
Emilio Esposito, Organizers
, Presiding
6:00 pm - 8:00 pm
  152 Oxygen diffusion pathways in a cofactor-independent oxygenase
Natali V Di Russo, Heather L Condurso, Steven D Bruner, Adrian E Roitberg.
  153 Effect of metal coordination environment on state-energy separations and paramagnetic chemical shifts in host-guest spin crossover complex models
William C Isley III, Salvatore Zarra, Tanya K Ronson, Rebecca K Carlson, Jonathan R Nitschke, Laura Gagliardi, Christopher J Cramer.
  165 Biomolecular modeling of synthetic Aβ protofilaments
Brendy Aoki, Patricia Soto.
  166 Computational exploration of the reactivity of isopenicillin N synthase
Victor Guang Ming Lee, Hrant P Hratchian.
  167 Molecular simulations of protein-protein and protein-lipid interactions during virus entry
D. Ploeger, Y Jewel, J Liu.
  168 MP2 and DFT study of the selectivity of NADP binding sites for novel ligands
Rachels Sanders, Mauricio Cafiero.
  169 MP2 and DFT analysis of the ligand selectivity of a sulfotransferase enzyme part 1: SULT 1A3
Diana Bigler, Larryn Peterson, Mauricio Cafiero.
  170 MP2 and DFT analysis of the ligand selectivity of a sulfotransferase enzyme part 2: SULT 1A1
Amelie H Weems, Diana Bigler, Larryn Peterson, Mauricio Cafiero.
  171 Role of solvation in the binding of morphine, met-enkephalin, and other ligands to the acetylcholine binding protein and µ opioid receptor
Katherine Hatstat, Mauricio Cafiero.
  172 Monte Carlo molecular simulation of surface binding density effects on DNA hybridization of two undecamer sequences
Matthijs van den Berg, John M Stubbs.
  173 H2 activation by PdO: The oxo ligand utility
Austin T Green
  174 Optimization strategy for anthrax toxin lethal factor (LF) inhibitors based on 3D-QSAR and pharmacophore models
Ting-Lan Chiu, Elizabeth A. Amin.
  175 Density functional theoretical study on the substituent effect in aryl halide oxidative additions to a Rh pincer complex
Young-Seuk Cho, Han Young Woo, Yongseong Kim, Sungu Hwang.
  176 Density functional theoretical study on the acid dissociation constant of an emissive analog of guanine
Yong-Jae Lee, Yun Hee Jang, Yongseong Kim, Sungu Hwang.
  177 Density functional theoretical study on the interchain packing in thiophene-benzothiadiazole based polymers
Sungu Hwang, Wonho Lee, Han Young Woo.
  178 Relative stability and diatropic character of carbaporphyrinoid systems
Deyaa I. AbuSalim, Timothy D. Lash.
  179 Biomolecular application for the correlation consistent composite approach: Noncovalent interactions for HF, NH3, H2O clusters
Amanda G Riojas, Ritwick Mynam, Tania E Bustillos, David A Carter, Angela K Wilson.
  180 Revisit of the reaction mechanism to form levoglucosan
Johnathan Henry, Brendan Leja, Dan Wang, Anthony Seitz, Jie Song.
  181 Trends in ROS-induced peptide backbone bond cleavage
Hannah M Stringfellow, Michael R Jones, Mandy C Green, Angela K Wilson, Joseph S Francisco.
  182 Reactivity of aldehyde with water at the interface and in bulk
Osamu Setokuchi
  183 Time-dependent density functional theory calculations of a solute with large amounts of explicit water
Enrique Alameda Jr, Christine M Isborn.
  184 Bioinformatics approach for the prediction of nitric oxide activation
John C Pearson
  185 Ab initio study of Mn and Co complexes for water splitting
Amendra Fernando Hewa Dewage, Christine M Aikens.
  186 Computational study of the energetics governing the regiochemistry of a 1,3-dipolar cycloaddition reaction
Phillip L. Esempio, Hernando A. Trujillo.
  187 WITHDRAWN
  188 Decomposition reactions of gold-phosphine complexes
KL Dimuthu M Weerawardene, Christine M Aikens.
  189 TDDFT magnetic circular dichroism spectra of Au9L83+ (L = PH3, PPh3) gold clusters
Natalia Karimova, Christine M Aikens.
  190 Theoretical study of direct amination of benzene on a Ni(111) surface
Zainab H Alsunaidi, Thomas R Cundari, Angela K Wilson.
  191 Rational design of metal organic frameworks for CO2 capture via computation
Michela L Brumfield, Angela K Wilson, Michael Drummond.
  192 Recovering nondynamic electron correlation energy for DFT
Chris C Jeffrey, Wanyi Jiang, Angela K Wilson.
  193 Vibrational scale factors for DFT using the polarization consistent basis sets
Matthew J Carlson, Marie L Laury, Angela K Wilson.
  194 Intermolecular effects and their influence on the 13C chemical shift anisotropy in organic crystal lattices
Zachary M Marsh, Matthew N. Srnec, Robbie J. Iuliucci, Jeffry D. Madura.
  195 New workflows from the Schrödinger materials science suite and their applications in quantum and classical simulation
Thomas F. Hughes
  196 DFT study shows proximal-pocket hydrogen bonds significantly influence mechanism of Compound I formation in chloroperoxidase
Armando D Pardillo, Alexander N Morozov, David C Chatfield.
  197 Inelastic neutron scattering of polyethylene measured at VISION: Comparison with first-principles simulation
Yongqiang Cheng, Christoph U Wildgruber, Lacy L Jones, Anibal J Ramirez-Cuesta.
  198 Strategies for lead inhibitor optimization: Application to HIVgp41
Brian C Fochtman, Robert C Rizzo.
  199 Trimethylamine adsorption on TiO2 anatase surfaces: New insights from a first-principles study
Leonardo Triggiani, Ana B Muñoz-García, Angela Agostiano, Michele Pavone.
  200 Pharmacophore-based scoring for DOCK: Application to HIVgp41
Lingling Jiang, Robert C. Rizzo.
  201 Computational approaches for targeting botulinum neurotoxins
Yuchen Zhou, Yu-Han Gary Teng, Brian E. McGillick, Subramanyam Swaminathan, Iwao Ojima, Robert C. Rizzo.
  202 Structure-based drug design employing solvated molecular footprints
Jiaye Guo, Robert C. Rizzo.
  203 Computational modeling of allostery and substrate binding in human glutathione synthetase
Brandall L. Ingle, Bisesh Shrestha, Myra D. Davis, Esmeralda Sandoval, Mary E. Anderson, Thomas R. Cundari.
  204 Structures and pKa values of acetamide and formamide related to natural bond orbitals and explicit water of hydration
Obsa L Bokku, Joseph L Alia.
  205 Theoretical investigations of the mechanism for ethylene addition to metal tristhiolate complexes and catalysts design
Haixia Li, Michael B Hall.
  206 Effect of functionalization of benzene by naphthyl and phenyl rings on cation-π interactions: A theoretical study
Ali Mirchi, Tandabany C. Dinadayalane, Jerzy Leszczynski.
  207 Computational tool for predicting structures of cyclic peptides
Hongtao Yu, Yu-Shan Lin.
  208 Multiple-timestep ab initio molecular dynamics
Ryan P. Steele
  209 Elucidating protonation states, intermolecular interactions, and reaction mechanisms that drive binding and specificity in DD-peptidases and β-lactamases
Jacqueline C Hargis, Sai L Vankayala, Justin K White, Henry L Woodcock.
  210 Computational studies on structures and reactivity of an osmium silylyne complex
Zhenggang Xu, Paul G Hayes, T. Don Tilley, Michael B Hall.
  211 Investigating absorption features and biradical character in open-shell organic compounds
Jacob Fosso Tande, Ozge Gunaydin-Sen, Peng Chen, Paul M Lahti, Janice L Musfeldt, Robert J Harrison.
  212 Conventional strain energies of bicycloalkanes and their methyl derivatives
Kaitlyn V. Kiss, Elizabeth M. Burns, David H. Magers.
  213 Noncovalent interactions in networks of trimethylamine-N-oxide, urea, and water
Leeann Smith, David H. Magers.
  214 Conventional strain energies of the diazetidines and the diphosphetanes
Shelley A. Smith, Ashley R. McDonald, Patricia H. Stewart, Glake Hill, David H. Magers.
  215 Relative stabilities of derivatives of 6-methylpentacene and 6-methylene-6,13-dihydropentacene
David H. Magers, Bei Cao.
  216 Classification of imbalanced PubChem BioAssay data using an efficient algorithm coupled with synthetic minority over-sampling technique
Ming Hao, Yanli Wang, Stephen H. Bryant.
  217 Molecular dynamics study on amphipathic drug interactions with the lipid bilayer
Stella D Koiki, Thuy Hien Nguyen, Zhiwei Liu, Preston B Moore.
  218 Rational design of platinum complexes with enhanced nonlinear optical properties
Dillon C. Yost, Svetlana Kilina, Kenneth Martin, Wenfang Sun.
  219 Practical procedure to calculate intermolecular interactions including statistical information between a protein and a large ligand
Hiroyuki Sato, Hajime Sugiyama, Yoshiaki Tanida, Azuma Matsuura, Shunji Matsumoto, Hiroaki Suga.
  220 Structure analysis of human red cell spectrin using homobifunctional chemical crosslinkers and high resolution mass spectrometry
Joshua I Rosario-Sepúlveda, Sandra Harper, Sira Srwiswasdi, David Speicher.
  221 Structural basis for Na+-sensitivity in dopamine D3 and D2 receptors
Mayako Michino, Lei Shi.
  222 Ligand- and structure-based characterization of protein-ligand interaction associated with Cdc2-like kinase 4 (Clk4) and dual specificity tyrosine-phosphorylation-regulated kinase 1A (Dyrk1A)
Yongmei Pan, Yanli Wang, Stephen Bryant.
  223 WITHDRAWN
  224 Calculating enthalpies of formation for amino derivatives of trinitrotoluene
Shelby L. Raines, Erica Q. Chong, Amika Sood, Glake Hill, David H. Magers.
  225 Feature-based calculation of the electrostatic component of the free energy of protein binding
Jacquelyn E Blum, Amelia B Kreienkamp, Finale Doshi-Velez, Mala L Radhakrishnan.
  226 Computational study of the proton affinity, 1H NMR chemical shifts, and thermophysical properties of imidazole derivatives for CO2 capture
Haining Liu, Zhongtao Zhang, Jason E Bara, C Heath Turner.
  227 Unified framework for computer-aided biologics design
Alain Ajamian
  228 Rationalizing non-standard interactions in ligand design: The duality of halogens
Chris Williams
  229 MD simulations reveal the impact of crystal packing on the post-SET loop of NSD1
Sara Tweedy, Sarah Graham, Heather Carlson.
  230 Quantifying the role of aromaticity in substituent effects of π-stacking
Jacob W G Bloom, Steven E Wheeler.
  231 Development of Web-based software for managing data in drug design
John C Faver, William L Jorgensen.
  232 Modeling the phosphoryl transfer reaction and transition state in the oncogenetically indicated GTPase protein RhoA and it's activating protein RhoA.GAP
Whitney F Kellett, Nigel G Richards.
  233 Computational models for improved estimation of highly plasma-protein-bound compounds
Jayeeta Ghosh, Michael Lawless, Marvin Waldman, Robert Clark, Walter Woltosz.
  234 Molecular dynamics simulations of human γD-crystallin aggregates found in cataracts
Sarah A Richards, Ralph A Wheeler.
  235 Effect of surface stoichiometry and passivating ligands on optical spectra of quantum dots
Mary M Hedrick, Dinusha Wadumesthrige, Svetlana Kilina.
  236 Alchemical free energy calculations for theophylline/caffeine to RNA aptamer with translationalharmonic restraints
Yoshiaki Tanida, Azuma Matsuura.
  237 Quantification of errors in modeling protein structures
Sonja B. Braun-Sand, Benjamin P. Martin, Christopher J. Brandon, James J. P. Stewart.
  238 Molecular dynamics study of Helicobacter pylori urease
Mona S Minkara, Melek N. Ucisik, Michael N. Weaver, Kenneth M. Merz.
  239 Molecular dynamics simulations of selective catalytic reduction of NOx over Cu-SSZ-13 zeolite
Eugenio Jaramillo, John F. McCleerey, George M. Psofogiannakis, Adri C. T. van Duin.
  240 Correlation between band gap and electronegativity of substituted atoms in the TiO2 crystalline structure
Andrew Glaid, Matthew Srnec, Jennifer Aitken, Jeffry Madura.
  241 How important is “p”-orbital in computational modeling
Nnenna Elechi, Daniel Tran, Andre M Darroux, Dennis Edwards, Hua-Jun Fan.
  242 Synthesis, characterization, and modeling of (E)-4,4'-(ethene-1,2-diyl) dianiline
Daniel Tran, Ian Shortt, Mykala Taylor, Odaro Adu, Yingchun Li, Hua-Jun Fan.
  243 Homology modeling of human concentrative nucleoside transporter 1 and virtual screening study to find novel hCNT1 inhibitors
Hemantkumar S Deokar, Hilaire C Playa, John K Buolamwini.
  244 Predictive combined study of similarity screening and kernel-based partial least squares model for kinase inhibitor activity and selectivity
Mrunalini H Deokar, Hemantkumar S Deokar, John K Buolamwini.
  245 15N vibrational frequency shifts of the cytochrome bc1 Reiske Iron-Sulfur Cluster distinguishes the protonation states of the imidazole side chains of histidine ligands
Benjamin R Jagger, Scott E Boesch, Ralph A Wheeler.
  246 Intermolecular interactions in molecular imprinting
Julia Saloni
  247 Investigation of the strength of the intramolecular hydrogen bond (IMHB) in pseudo-chair carboxyphosphate
Sarah E Kochanek, Steven M Firestine, Jeffrey D Evanseck.
  248 Quantification of errors in semiempirical methods when used to study protein structures
Benjamin P. Martin, Christopher J. Brandon, James J. P. Stewart, Sonja B. Braun-Sand.
  249 Piezo-response in hydrogen-bonded organic systems: Development of a design rationale and screening method
Keith A Werling, Maryanne L. Griffin, Geoffrey R. Hutchison, Daniel S. Lambrecht.
  250 Charge delocalization in copper (I) and copper (II) dithione complexes
Marissa McGovern, Benjamin Mogesa, Partha Basu, Ralph A Wheeler.
  251 Electron transport in porphyrin-based OPV donor materials: A computational study
Morgan A. Hammer, Zachary L. Dunn, Benjamin J. Topham, Trilisa M. Perrine.
  252 Molecular simulation study of the surface tension of curved interfaces
Amir Taghavi Nasrabadi, Steven O. Nielsen.
  253 Isotope effects and dynamics in the decarboxylation of b-ketoacids: Lifetime and the nature of acid catalysis
Hannah Aziz, Daniel Singleton.
  254 Structural and energetic analysis of carboxyphosphate
Traci M Clymer
  255 Multi-scale computational modeling of morphology and charge mobilities of self-assembled donor oligomers in different crystalline phases
ilhan Yavuz, Blanton Martin, Jiyong Park, Kendall N. Houk.
  256 Atomic-scale modelling of hydrogen storage in the UiO-66 and UiO-67 metal-organic frameworks
Stefan Andersson, Per-Erik Larsson.
  257 Impact of metal ions in metal(II)-polypyridine dyes on charge transfer mechanisms in dye functionalized CdSe quantum dots
Peng Cui, Svetlana Kilina.
  258 Parallel Fortran program for performing density derived electrostatic and chemical (DDEC) analysis
Nidia G Gabaldon Limas, Thomas A Manz.
  260 MD simulation studies of gatekeeper - inhibitor interactions: Toward molecular basis of selectivity profile of EGFR inhibitors
Jiyong Park, Joseph McDonald, Russell Petter, Kendall N. Houk.
  261 Theoretical study of the formation of some CO2-(nitrogen heterocycles) adducts
Elizabeth Hernandez-Marin, Adela Lemus-Santana.
  262 Mechanistic implication on RNA transphosphorylation from model reaction kinetic isotope effects: A computational study
Haoyuan Chen, Timothy J Giese, Ming Huang, Kin-Yiu Wong, Darrin M York.
  263 Functional classification of six-hairpin glycosidase superfamily with structurally aligned local sites of activity
Ramya Parasuram, Mary Jo Ondrechen.
  264 Cluster analysis of molecular dynamics trajectories in protein adsorption simulations
Tigran Abramyan, Steven J Stuart, Robert A Latour.
  265 Thermochemical study of perhalocarbons
Kameron R. Jorgensen
  266 Localization of virtual molecular orbitals: Projection vs. direct optimization
Alexander Gaenko, Mark S Gordon.
  267 Chemocentric informatics analysis of "omics" data identifies novel chemical-gene-disease associations in autism
Rima Hajjo, Alexander Tropsha.
  268 GPU-based protein-protein docking with FFT
David R Hall
  269 Ligand binding site identification in membrane-bound oncogenic K-ras
Priyanka P Srivastava, Alemayehu A Gorfe.
  270 C-H activation of Cp-Ir(RH)(CO) and Cp*-Ir(RH)(CO)
Nnenna Elechi, Hua-Jun Fan, Michael B Hall, Amanda Renz.
  271 WITHDRAWN
  272 Molecular modeling of zwitterionic agonists of Sphingosine 1-phosphate receptor 1 (S1PR1)
Michael J Ferracane, Kevin R Lynch, Timothy L Macdonald.
  273 Robust quantum-chemical description of organic two-center mixed-valence systems
Christopher A Sutton, Thomas Körzdörfer, Jean-Luc Brédas, Veaceslav Coropceanu.
  274 Computer-aided identification of rhodanine derivatives with activity against Staphylococcus aureus type II topoisomerase
Malela M. Werner, Zhiyu Li, Randy J. Zauhar.
  275 Periodic DFT analysis of Fe-MOF-74 and new structures derived from activation with N2O
Joshua D Borycz, Joachim Paier, Laura Gagliardi.
  276 WITHDRAWN
  277 R.E.D. Python: Object oriented programming for Amber force fields
Fan Wang, Jean-Paul Becker, Piotr Cieplak, Francois-Yves Dupradeau.
  278 Understanding dynamic structural variations in HIV-1 envelope glycoprotein Gp120
Tuoling Qiu, David F. Green.
  279 Utilizing density embedding schemes for the calculations on organic molecular crystals
Benjamin J Albrecht, Keith A Werling, Daniel S Lambrecht.
  280 Computational investigation of ligand encapsulation in helical foldamers
Ara M. Abramyan, Zhiwei Liu, Vojislava Pophristic.
  281 Filtering decoy poses using QSAR models improves the accuracy of ligand ranking by molecular docking
Regina Politi, Denis Fourches, Alexander Tropsha.
  282 Polarizable force field for the simulation of face-centered cubic metals and biological interfaces
Hadi Ramezani-Dakhel, Isidro Lorenzo Geada, Marialore Sulpizi, Hendrik Heinz.
  284 Evolution of metalloenzymes through multi-scale dynamics modeling
Anastassia N. Alexandrova, Crystal E. Valdez, Manuel Sparta.
  285 WITHDRAWN
  286 Li defects in solid electrolyte and in electrode/electrolyte interface: A first-principles study
Santosh KC, Roberto C Longo, Ka Xiong, Kyeongjae Cho.
  287 New force field development for terminal-modified PEO molecules
Siyan Chen, Wenmei Gao, Shasha Yi, Zhonghan Hu.
  288 Rigorous error bounds for Ewald summation of electrostatics at planar interfaces
Cong Pan, Zhonghan Hu.
  289 Oxidative cleavage of the C-H, C-C, C-O bonds by transition metal atoms
Jiaqi Wang, Angela K Wilson.
  290 WITHDRAWN
  291 Development of the CHARMM inteface and graphics Web User Interface as a platform for comptuer aided drug design
Yuri Pevzner, Vinushka Schalk, Benjamin T Miller, Henry L Woodcock.
  292 Molecular simulations of the hepatitis delta virus ribozyme: Interplay of metal binding, nucleobase pKa's, and catalysis
Brian K Radak, Taisung Lee, Michael E Harris, Darrin M York.
  293 Computer-aided study of hidden potential in Traditional Indian Medicine Ayurveda
Vladimir Poroikov, Dmitry Filimonov, Alexey Lagunin, Dmitry Druzhilovskiy, Dinesh Gawande, Rajesh Goel.
  294 Extended Hirshfeld: Atomic charges that combine accurate electrostatics with transferability
Toon Verstraelen, Paul W Ayers, Veronique Van Speybroeck, Michel Waroquier.

COMP, Emilio Esposito, Scott Wildman Sunday, March 16, 2014

Quantum Chemistry - AM Session Start the #ACSdallas Meeting Off Right with the Application of Quantum Chemistry #methodMadness
Omni Dallas Hotel
Room: Fair Park 2
Cosponsored by CINF, PHYS
Eric Patterson, Organizers
Michael Jones, Presiding
8:30 am - 11:45 am
8:30 19 Calculation of enthalpies of formation:2 Hydroxyl- and carbonyl-compounds
Radu Bacaloglu, Livius Cotarca.
9:00 20 Current status of the project to enable Gaussian 09 on GPGPUs
Roberto Gomperts, Michael Frisch, Giovanni Scalmani, Brent Leback.
9:30 21 Gas phase acylation of substituted phenols: The borderline between BAC2 and concerted nucleophilic acyl substitution
Andrew J Franjesevic, Justin B Houseknecht.
10:00   Intermission
10:15 22 QTAIM analysis and anharmonic vibrational spectroscopy studies of novel molecules containing heavy rare gases
Amelia Fitzsimmons, Mariusz Klobukowski.
10:45 23 Simulating the photochemistry of nitrate in snow by electronic structure calculations
Keith T Kuwata
11:15 24 Mechanism on remarkably stereospecific monochlorination of adamantylideneadamantane
Ren Feng, Jing Kong, Dieter Lenoir, Ji-Jun Zou, Li Wang, Paul von Ragué Schleyer.

COMP, Emilio Esposito, Scott Wildman Sunday, March 16, 2014

Quantum Chemistry - PM Session A Whole day of #quantumChemistry Application Talks! #lucky :D
Omni Dallas Hotel
Room: Fair Park 2
Cosponsored by CINF, PHYS
Eric Patterson, Organizers
Seonah Kim, Presiding
1:30 pm - 5:15 pm
1:30 45 Action of a broad spectrum antiviral medication against human herpes: A quantum chemical investigation
Andrew J Perla, Michael J Szatkowski, Loredana Valenzano.
2:00 46 Assembling the peptidoglycan bacterial cell wall: A stepwise quantum chemical approach
Daniel T Beegle, Kapil Adhikari, Loredana Valenzano.
2:30 47 Quantum mechanical study of a copper-dependent lytic polysaccharide monooxygenase active site
Seonah Kim, Robert S Paton, Miao Wu, Jerry Ståhlberg, Mats Sandgren, Gregg T Beckham.
3:00 48 Analytical harmonic vibrational frequencies for the green fluorescent protein computed with ONIOM: Chromophore mode character and its response to environment
Lee M Thompson, Paul M Champion, J. Timothy Sage, Michael J Frisch, Jasper J. van Thor, Michael J Bearpark.
3:30   Intermission
3:45 49 Conjugate additions of nucleophilic amino acids to enone containing inhibitors: A DFT study
Nihan Celebi-Olcum
4:15 50 Phosphoryl transfers of tyrosyl DNA-phosphodiesterase I: A quantum mechanical “cluster model” study
Nathan J. DeYonker, Charles Edwin Webster.
4:45 51 Elucidating the thiamine diphosphate activation mechanism in 1-deoxy-d-xylulose 5-phosphate synthase: A hybrid QM/MM reaction path study
Justin K White, Henry L Woodcock.

COMP, Emilio Esposito, Scott Wildman Monday, March 17, 2014

Quantum Chemistry - AM Session Providing Awesome #quantumChemistry Talks for as Long as I Can Remember
Omni Dallas Hotel
Room: Fair Park 2
Cosponsored by CINF, PHYS
Eric Patterson, Organizers
Robert Paton, Presiding
8:30 am - 11:45 am
8:30 69 Adsorption of light hydrocarbons in metal-organic frameworks: Computational study at quantum chemical level
Gemechis D Degaga, Loredana Valenzano.
9:00 70 Application of a pseudopotential-based composite method for first and second row transition metal thermochemistry
Sivabalan Manivasagam, Marie L Laury, Angela K Wilson.
9:30 71 Mechanisms of copper-catalyzed water oxidation: Theoretical insights
Stuart Winikoff, Christopher Cramer.
10:00   Intermission
10:15 72 Effects of CO and NO on TiO2 supported Pt, Pd, and Rh nanoparticle disintegration
Bryan R Goldsmith, Evan Sanderson, Runhai Ouyang, Wei-Xue Li.
10:45 73 Mechanistic studies of water oxidation catalyzed by the β-MnO2 (110) surface
Mikhail Askerka, Mehmed Z Ertem, Victor Batista, John Tully.
11:15 74 Computational investigation of M-Ga-F triatomics with row 3 metals (M=Sc … Zn)
Shesha A Shah, Nathan J. DeYonker.

COMP, Emilio Esposito, Scott Wildman Monday, March 17, 2014

Quantum Chemistry - PM Session Is #quantumChemistry Methodologies Really #methodMadness or Just Serious Math?
Omni Dallas Hotel
Room: Fair Park 2
Cosponsored by CINF, PHYS
Eric Patterson, Organizers
Traci Clymer, Presiding
1:30 pm - 5:15 pm
1:30 95 First-principles studies on photonic properties of PLED materials
Huai-Wen Tsai, Che-Wun Hong.
2:00 96 Ab initio framework for uncovering structure-property relationships of amorphous catalysts
Bryan R. Goldsmith, Evan D Sanderson, Daniel Bean, Baron Peters.
2:30 97 Computational quantum chemistry analysis of the cathodic catalyst in low temperature fuel cells
Chun-Ting Liu, Che-Wun Hong.
3:00 98 Screened hybrid density functionals for heterogeneous catalysis
John J Determan, Benjamin G Janesko.
3:30   Intermission
3:45 99 Chemical semantics: A semantic web start-up for pubishing computational chemistry data obtained from ab initio calculations
Neil S Ostlund, Mirek Sopek.
4:15 100 Local probes of the one-particle density matrix: Interpretive tools and "Rung 3.5" density functionals
Benjamin G. Janesko
4:45 101 Improved density functionals: Better chemistry from minimal empiricism
Narbe Mardirossian, Martin Head-Gordon.

COMP, Emilio Esposito, Scott Wildman Tuesday, March 18, 2014

Quantum Chemistry - AM Session .@acsCOMP Has Always Supported #quantumChemistry. Check Out the QC Applications
Omni Dallas Hotel
Room: Fair Park 2
Cosponsored by CINF, PHYS
Eric Patterson, Organizers
Yuchen Zhou, Presiding
8:30 am - 11:45 am
8:30 119 Influence of (Mg, Al, Fe) impurities on triclinic Ca3SiO5: Interpretations from DFT calculations
Jian Huang, Loredana Valenzano, Gaurav Sant.
9:00 120 Mimicking thermal effects on bulk properties of molecular crystal polymorphs and cleaving their surfaces from first principles
Kapil Adhikari, Kenneth M Flurchick, Loredana Valenzano.
9:30 121 Sigma hole bonding and the stability of inorganic adducts
Kelling Donald
10:00   Intermission
10:15 122 Utility of new generations of coupled-cluster methods and algorithms in catalytic and structural properties of gold nanoparticles
Piotr Piecuch, Jared A. Hansen, Masahiro Ehara, Benjamin G. Levine.
10:45 123 Intriguing lithiation behavior of Si-rich oxides: A first principles study
Chia-Yun Chou, Gyeong S. Hwang.
11:15 124 Electric dipole moment of HBr: A comparison of relativistic all-electron and pseudopotential calculations
Robert Hinde, Nabil Saleh.

COMP, Emilio Esposito, Scott Wildman Tuesday, March 18, 2014

Quantum Chemistry - PM Session Creating and Expanding #quantumChemistry Methods
Omni Dallas Hotel
Room: Fair Park 2
Cosponsored by CINF, PHYS
Eric Patterson, Organizers
Rebecca Weber, Presiding
1:30 pm - 4:45 pm
1:30 145 Improving the computational efficiency of DFT-derived net atomic charges for flexible force fields of biological materials
Nidia G Gabaldon Limas, Thomas A Manz.
2:00 146 Tensors of dynamic polarizabilities calculated in TDHF/TDDFT schemes with multiresolution multiwavelet basis sets
Yukina Yokoi, Hideo Sekino, Jeff R. Hammond, Álvaro Vázquez-Mayagoitia.
2:30 147 Combining active-space coupled-cluster approaches with moment energy corrections via the CC(P;Q) methodology: Connected triple and quadruple excitations
Piotr Piecuch, Jun Shen, Nicholas P. Bauman.
3:00   Intermission
3:15 148 Two-step multireference approaches to efficiently model electronic excited states
Benjamin G Levine, Yinan Shu.
3:45 149 New wavefunction forms for strong electron correlation inspired by the eigenvectors of exactly solveable model systems: The importance of symmetry-broken solutions
Paul W. Ayers, Katharina Boguslawski, Pawel Tecmer, Peter A. Limacher, Paul A. Johnson, Stijn De Baerdemackers, Dimitri Van Neck, Patrick Bultinck.
4:15 150 Correlation consistent basis sets: The atoms In-Xe
Andrew Mahler, Angela K Wilson.

COMP, Emilio Esposito, Scott Wildman Wednesday, March 19, 2014

Quantum Chemistry - AM Session Last Chance for #quantumChemistry Applications at #ACSdallas #packTheRoom
Omni Dallas Hotel
Room: Fair Park 2
Cosponsored by CINF, PHYS
Eric Patterson, Organizers
Kameron Jorgensen, Presiding
8:30 am - 11:45 am
8:30 310 Heavy atom tunneling on carbene and anti-aromatic systems
Sebastian Kozuch, Weston T. Borden.
9:00 311 How to make the σ0π2 singlet the ground state of carbenes
Bo Chen, Andrey Yu. Rogachev, David A. Hrovat, Roald Hoffmann, Weston Thatcher Borden.
9:30 312 Exploring potential energy landscapes of mechanosensitive materials
Sai Sriharsha M Konda, Dmitrii E Makarov.
10:00   Intermission
10:15 313 First principles prediction of an insensitive high energy density material
Barak Hirshberg, Chagit Denekamp.
10:45 314 Sandwich-like aggregates of highly-reduced corannulene: Theoretical study of their formation and electronic structure
Andrey Rogachev, Marina Petrukhina.
11:15 315 Predicting paramagnetic chemical shifts and state-energy separations in host-guest spin crossover complexes
William C Isley III, Salvatore Zarra, Tanya Ronson, Rebecca Carlson, Jonathan R Nitschke, Laura Gagliardi, Christopher J Cramer.

COMP, Emilio Esposito, Scott Wildman Wednesday, March 19, 2014

Quantum Chemistry - PM Session Quantum Dynamics and Monte Carlo Simulations to finish #ACSdallas with awesome
Omni Dallas Hotel
Room: Fair Park 2
Cosponsored by CINF, PHYS
Eric Patterson, Organizers
Jiaye Guo, Presiding
1:00 pm - 4:45 pm
1:00 339 Role of the second coordination sphere in selectivity of O2 reduction with Fe porphyrins: An ab-initio MD perspective
Aaron W Pierpont, Derek Wasylenko, Simone Raugei, James M Mayer.
1:30 340 Roaming trajectories in a reduced-dimensional model of ketene isomerization
Inga S. Ulusoy, John F. Stanton, Rigoberto Hernandez.
2:00 341 Multidimensional quantum dynamics of an amide I vibrational excitation in a model peptide chain
Holly Freedman, Gabriel Hanna.
2:30   Intermission
2:45 342 Accelerated ab initio sampling and molecular dynamics
Ryan P. Steele
3:15 343 Accurate zero-point energies for Ar monolayers adsorbed on MgO(100)
Robert Hinde
3:45 344 Quantum Monte Carlo study of hcp solid 4He: Searching for anisotropy in the Debye-Waller factor
Ashleigh Barnes, Robert Hinde.
4:15 345 Density functional calculations of an inhomogenous 4He system
Matthew Dutra, Robert Hinde.

COMP, Emilio Esposito, Scott Wildman Sunday, March 16, 2014

Tracing Pathways in Biomolecular Simulation - AM Session
Omni Dallas Hotel
Room: Trinity 7
Cosponsored by BIOL, CINF, MEDI, PHYS
Chung Wong, Ronald Levy, Organizers
Emilio Gallicchio, Presiding
8:30 am - 11:45 am
8:30 1 Folding@home: Simulating pathways in atomic detail on the seconds timescale, with applications to kinase conformational change and protein folding
Vijay Pande
9:00 2 From protein folding to biomolecular machines of life
Jose N Onuchic, Biman Jana.
9:30 3 Equilibrium thermodynamics and folding kinetics of a short, fast-folding, beta-hairpin
Camilo A Jimenez-Cruz, Angel E Garcia.
10:00   Intermission
10:15 4 How long does it take to equilibrate the unfolded state of a protein?
Ronald M Levy, Nan-jie Deng, Wei Dai.
10:45 5 Molecular and coarse-grained views of protein dynamics in the unfolded state
Dmitrii E Makarov
11:15 6 Simulating millisecond dynamics of RNA polymerase II translocation at atomic resolution using Markov State models
Xuhui Huang

COMP, Emilio Esposito, Scott Wildman Sunday, March 16, 2014

Tracing Pathways in Biomolecular Simulation - PM Session
Omni Dallas Hotel
Room: Trinity 7
Cosponsored by BIOL, CINF, MEDI, PHYS
Chung Wong, Ronald Levy, Organizers
Chung Wong, Presiding
1:30 pm - 4:45 pm
1:30 25 Long molecular dynamics simulations of proteins: Progress, promise, and problems
David E. Shaw
2:00 26 Modeling the function and directionality of molecular motors and other challenging biological systems
Arieh Warshel
2:30 27 Enhanced sampling by accelerated molecular dynamics
J. Andrew McCammon
3:00   Intermission
3:15 28 Application of the string method to map conformational transitions in large biomolecular systems
Benoit Roux, Mikolai Fajer, Avisek Das, Yilin Meng.
3:45 29 Phosphate release coupled to rotary motion of F1-ATPase
Kei-ichi Okazaki, Gerhard Hummer.
4:15 30 Atomistic and coarse-grained simulations of the self-assembly of the tau peptide
Joan-Emma Shea

COMP, Emilio Esposito, Scott Wildman Monday, March 17, 2014

Tracing Pathways in Biomolecular Simulation - AM Session
Omni Dallas Hotel
Room: Trinity 7
Cosponsored by BIOL, CINF, MEDI, PHYS
Chung Wong, Ronald Levy, Organizers
Chung Wong, Presiding
8:30 am - 11:45 am
8:30 52 Weighted ensemble simulation methodology: Progress and challenges
Daniel M Zuckerman
9:00 53 Atomistic simulation of protein-peptide binding with rigorous kinetics
Lillian Chong
9:30 54 Learning about transitions: Adaptive controls for the molecular dynamics database
Thomas B Woolf, Yanif Ahmad, Sarana nutanong, I-Jeng Wang.
10:00   Intermission
10:15 55 Determining reaction paths from milestoning calculations
Ron Elber
10:45 56 Orthogonal space sampling methods to enable quantitative free energy simulations
Wei Yang
11:15 57 Conformational and alchemical pathways in extended ensemble binding free energy calculations
Emilio Gallicchio, Peng He, Lauren Wickstrom, Nanjie Deng, Ronald M Levy.

COMP, Emilio Esposito, Scott Wildman Monday, March 17, 2014

Tracing Pathways in Biomolecular Simulation - PM Session
Omni Dallas Hotel
Room: Trinity 7
Cosponsored by BIOL, CINF, MEDI, PHYS
Chung Wong, Ronald Levy, Organizers
Lillian Chong, Presiding
1:30 pm - 4:45 pm
1:30 75 Understanding the role of acid in cellular processes with molecular simulations
Charles L. Brooks III
2:00 76 Calculation of ion permeation through biological ion channels via course-grained models employing atomic level input
Rob D. Coalson
2:30 77 Markov State Models of ATP movement across the mitochondrial membrane
Michael Grabe
3:00   Intermission
3:15 78 Induced fit effects and water structure in modeling ligand binding to proteins: Conformational sampling, free energy perturbation molecular dynamics simulations, and kinetics of binding
Richard A Friesner
3:45 79 Analysis of energy landscapes governing protein-protein association
Sandor Vajda, Dima Kozakov, Dmitri Beglov, Ioannis Ch Paschalidis, Pirooz Vakili.
4:15 80 Protein-protein interactions in the activity of inhibitor of κB kinase-β
Michael R Jones, Angela K Wilson.

COMP, Emilio Esposito, Scott Wildman Tuesday, March 18, 2014

Tracing Pathways in Biomolecular Simulation - AM Session
Omni Dallas Hotel
Room: Trinity 7
Cosponsored by BIOL, CINF, MEDI, PHYS
Chung Wong, Ronald Levy, Organizers
Chung Wong, Presiding
8:30 am - 11:45 am
8:30 102 Molecular simulations of MAb-MAb association
Mauro Lapelosa, Tom Patapoff, Dan Zarraga.
9:00 103 Electrostatic channeling of dihydrofolate in the dihydrofolate reductase/thymidylate synthase complex
Peter M Kekenes-Huskey, Changsun Eun, Vince T Metzger, James A McCammon.
9:30 104 High-level QM/MM free energy calculations at affordable computational cost
Gerhard Koenig, Phillip Hudson, Stefan Boresch, Henry L Woodcock.
10:00   Intermission
10:15 105 Molecular dynamics simulations of the activated cannabinoid CB2 receptor in complex with the inhibitory Gαi1β1γ2 protein
Jagjeet Singh, Diane Lynch, Alan Grossfield, Nicholas Leioatts, Michael Pitman, Patricia Reggio.
10:45 106 Binding mode analysis of Sterol 24-C methyltransferase by docking and molecular dynamics simulation
Asma Abro, Syed Sikander Azam.
11:15 am 107 WITHDRAWN

PRES, Thomas Barton Monday, March 17, 2014

Benefits of Chemistry in our Lives - AM Session
Sheraton Dallas
Room: Austin Blrm 2
Cosponsored by AGFD, AGRO, CHAS, CINF, CPRC, ENFL, ENVR, HIST, I&EC, MEDI, PMSE, POLY
Donna Nelson, Attila Pavlath, Organizers
Attila Pavlath, Donna Nelson, Presiding
8:00 am - 10:20 am
8:00 7 Why is it important to maintain the public image of chemistry?
Thomas Barton
8:10 8 Contributions of chemistry to energy and transportation
William F. Carroll
8:35 9 Conversations on chemistry and the environment: Engaging chemists and the public
Bassam Z Shakhashiri
9:00 10 Communication and entertainment without chemistry
Attila Pavlath
9:25 11 Bio-responsive molecules: Formidable weapons in medicine's arsenal
Ned Heindel
9:50 12 How chemistry has improved our food supply
Elizabeth Ann Nalley
10:15   Concluding Remarks

 

Technical Program with Abstracts

  • 10880 reads

ACS Chemical Information Division (CINF)
247th ACS National Meeting, Spring 2014
Dallas, TX (March 16-20, 2014)

CINF Symposia

E. Bolstad, Program Chair

[Created Fri Feb 14 2014, Subject to Change]

Sunday, March 16, 2014

Joint CINF-RSC CICAG Symposium: Chemical Schemas, Taxonomies and Ontologies - AM Session
Ontologies and Substances

Omni Dallas Hotel
Room: Deep Ellum A
Cosponsored by COMP, MEDI, ORGN, PHYS
Antony Williams, Jeremy Frey, Simon Coles, Leah McEwen, Organizers
Jeremy Frey, Presiding
8:30 am - 11:55 am
8:30 Introductory Remarks
8:45 1 Bridging worlds: Speaking multiple scientific languages

Jessica Peterson1, J.Peterson@elsevier.com, Pieder Caduff2, David Evans2, Juergen Swienty-Busch3. (1) Elsevier Inc, Philadelphia, United States, (2) Reed Elsevier Properties SA, Neuchâtel, Switzerland, (3) Elsevier Information Systems GmbH, Frankfurt, Germany

Cross-scientific communication and actionable information are some of the biggest hurdles when research teams need to take critical decisions. Each scientific sub-discipline uses their very own specific and idiosyncratic vocabularies and nomenclatures. Enabling effective interdisciplinary communication either between applications or within a single framework requires extensive cross mapping of taxonomies, data normalization and ontological relationships harmonization. Better decisions, fewer errors, quicker results are results interdisciplinary teams can achieve when such methods and networks are put in place. We present our experiences leading up to interoperable functionality across two disparate research tools through small molecule taxonomy mapping

9:10 2 Ontology-driven information system for chemical and materials science

Nico Adams1, nico.adams@csiro.au, Murray Jensen1, Danielle Kennedy1, Cornelius Kloppers2, Yanfeng Shu2, Claire D'Este2, Craig Lindley2. (1) Materials Science and Engineering, CSIRO, Clayton, Victoria 3150, Australia, (2) Computational Informatics, CSIRO, Hobart, Tasmania 7001, Australia

Standard information systems for the chemical and materials sciences are almost entirely predicated on the notion of chemical structure and composition as the unique criterion of identity, which also encodes properties. However, the properties of many extended materials, such as polymers (including coordination polymers) are not comprehensible on the basis of their chemical structure and composition alone – rather they are often determined by the provenance and processing history of a material. The melting points of polymers, for example, can be significantly changed through a simple post-processing step such as compounding – this changes property-determining intermolecular interactions rather than fundamental chemistry and as such is not encoded by simple structure representations. This, in turn, means that chemical and process descriptions need to be interoperable and associable with chemical objects. Ontologies map particularly well onto the problem of developing integrated chemical and process representation of entities and can be used to develop complete provenance traces of materials. In this talk, we will discuss our approach to developing such representations and how they can be leveraged for multiple purposes in materials information systems.
9:35 3 Open ontologies and chemical characterization

Colin Batchelor1, Leah R McEwen2, lrm1@cornell.edu. (1) Royal Society of Chemistry, Cambridge, United Kingdom, (2) Cornell University, Ithaca, NY 14850, United States

Cheminformatics techniques afford us opportunity to create tools and protocols that can allow chemists to ask sophisticated questions of the expanding corpus of chemical literature and data and return relevant and well-organized results. One of the most formulaic, and therefore most tractable, parts of the chemistry article is the characterization data for organic syntheses. We provide a worked example of how open ontologies from the RSC, EBI and elsewhere can be used to describe characterization data for a given synthesis, and discuss advantages for elucidating and amassing reported data from the literature. We consider options and outstanding challenges in engaging bench chemists in extending this work to less formulaic areas of the literature, such as full reaction schema and materials specification, mining the primary literature in such a way to suggest recognizable patterns to chemists.
10:00 Intermission
10:15 4 FDA terminology for substances

Yulia Borodina, yulia.borodina@fda.hhs.gov, Larry Callahan, Frank Switzer, Bill Hess, Randy Levin. Office of the Commissioner, FDA, Silver Spring, MD 20993, United States

FDA has started publishing a controlled terminology for substances used in medicinal products. The terminology supports types of substances described in the ISO IDMP 11238 standard. It is implemented as an extension of the Structured Product Labeling (SPL) markup standard and is internally known as “Substance Indexing.” Indexing refers to the creation by FDA of one or more files with machine-readable annotations that can be linked to the product SPL provided by the company. These machine-readable tags in SPL format allow the information to be easily incorporated, based on assigned codes, into electronic health records, e-prescribing systems, pharmacovigilance and clinical decision support systems for rapid searching, sorting of, and access to, relevant product information needed to make critical health care decisions and enhance patient care. A Substance Index File contains information about one substance concept. It includes the substance definition and the unique identifier (UNII) assigned by the FDA Substance Registration System. For most substances, the definition includes a representation of their molecular structure. Chemical substances and mixtures of chemical substances are defined by one or more chemical structures representing structural units or moieties that constitute the substance. Each chemical structure is accompanied by the IUPAC International Chemical Identifier (InChI). Definitions of proteins and nucleic acids include structural units represented using a single letter notation. These and other defining characteristics and their relationships will be discussed.
10:40 5 Pipeline for automated structure-based classification in the ChEBI ontology

Janna Hastings, hastings@ebi.ac.uk, Venkatesh Muthukrishnan, John W May, Gareth Owen, Christoph Steinbeck. Cheminformatics and Metabolism, European Bioinformatics Institute, Cambridge, Cambridgeshire CB10 1SD, United Kingdom

ChEBI is a database and ontology of chemical entities of biological interest. As of October 2013, it contains more than 35,500 entries, organised into structure-based and role-based classification hierarchies. Each entry is extensively annotated with a name, definition and synonyms, other metadata such as cross-references, and chemical structure information where appropriate. In addition to the classification hierarchy, the ontology also contains diverse chemical and ontological relationships. While ChEBI is primarily manually maintained, recent developments have focused on improvements in curation through partial automation of common tasks. We will describe a pipeline we have developed for structure-based classification of chemicals into the ChEBI structural classification. The pipeline connects class-level structural knowledge encoded in Web Ontology Language (OWL) axioms as an extension to the ontology, and structural information specified in standard representations. We make use of the Chemistry Development Kit, the OWL API and the OWLTools library. Harnessing the pipeline, we are able to suggest the best structural classes for the classification of novel structures within the ChEBI ontology.
11:05 6 Accessing Open PHACTS: Interactive exploration of compounds and targets from the semantic web

Katrin Stierand1, stierand@zbh.uni-hamburg.de, Tim Harder3, Lothar Wissler2, Christian Lemmen2, Matthias Rarey1. (1) ZBH Center for Bioinformatics, University of Hamburg, Hamburg, 20146 Hamburg, Germany, (2) BioSolveIT GmbH, St. Augustin, Germany, (3) Philips Medical Systems DMC GmbH, Hamburg, Germany

Pharmacological research is hampered by scattered data which have to be retrieved by varying methods and in different data formats. This heterogeneity increases research costs and limits throughput. Over the last two years, the Open PHACTS Discovery Platform has been developed as a centralized repository, integrating pharmacological data from a variety of information resources and providing tools and services to query these integrated data in pharmacological research. Here, we present the ChemBioNavigator (CBN), a web application allowing to navigate the Open PHACTS chem-bio space with a focus on small molecules and their targets. CBN comprises of a large visualization area with different view modes and two information panels, allowing a deeper insight in information for compounds and targets. It allows interactive exploration of compound sets through sorting and subset selection as well as extending sets by substructure or similarity search. The relation between compounds and targets is defined by assay data from the Discovery Platform. Each compound and each target is annotated with information from multiple data sources which is provided together with the provenance for each data point. In this contribution we roughly outline the CBN technology and highlight the advantages of exploiting the integrated data through the CBN's smart and intuitive interface.
11:30 7 Machine-processable representation and applications of the Globally Harmonized System

Mark I Borkum, m.i.borkum@soton.ac.uk, Department of Chemistry, University of Southampton, Southampton, Hampshire SO17 1BJ, United Kingdom

The Globally Harmonized System of Classification and Labelling of Chemicals, or GHS, is an international standard, created by the United Nations, designed to supersede the many classification and labelling systems that are currently in use around the world. In the European Union, the GHS is implemented as the CLP Regulation. One of the barriers to the adoption of the GHS is the requirement for organisations to map the classification and labelling elements of their existing systems onto those of the GHS. A requirement that, from June 2015, will be mandatory for any organisation that operates within the European Union. We present a software system for the semi-automatic extraction and enrichment of a machine-processable controlled vocabulary of classification and labelling elements from the information content of the CLP Regulation, along with an exemplar dataset of descriptions of substances and mixtures. As our software system uses Semantic Web technologies, the resulting data is highly amenable to further manipulation and integration with data from other sources.

Sunday, March 16, 2014

Joint CINF-CSA Trust Symposium: Energy Information Resources to Help Catalyze Your Research - AM Session

Omni Dallas Hotel
Room: Deep Ellum B

Grace Baysinger, Organizers
Grace Baysinger, Presiding
8:30 am - 11:55 am
8:30 Introductory Remarks
8:35 8 Trends in bio-based chemicals: Business intelligence from published literature

Steve M Watson, s.watson@elsevier.com, Alternative Energy, Elsevier, Amsterdam, North Holland 1043NX, The Netherlands

A new information solution, Elsevier Biofuel, has been used to review the literature landscape, revealing trends in R&D towards the production of valuable chemicals from biomass. Elsevier Biofuel comprises advanced search and analysis tools, using a domain specific taxonomy to automatically classify over 21 million documents, many in full text, covering relevant journal publications, patents, technical reports, conference proceedings and trade publications. The analysis highlights emerging technology areas, commercial opportunities, and the leading companies staking a claim to this space.
9:05 9 Chemistry databases and alerting services for finding the best energy research content

Serin Dabb1, dabbs@rsc.org, Richard Kidd2. (1) Royal Society of Chemistry, Cambridge, Cambridgeshire CB4 0WF, United Kingdom, (2) Royal Society of Chemistry, Cambridge, Cambridgeshire CB4 0WF, United Kingdom

Chemistry research underpins the pursuit of sustainable and renewable materials for energy generation and storage. Due to the interdisciplinary nature of energy research, tools are needed to provide relevant chemically related content to a researcher in this field, whether they have a chemistry background or not. As with all fields of research, services which condense validate, or filter information are even more valuable due the sheer quantity of information available on-line. Current literature updating services (such as Catalysts and Catalysed Reactions), highly curated information (such as The Merck Index Online), or information aggregators (such as ChemSpider), are all useful portals for energy researchers to find chemical information. This talk will outline the different types of content and subject coverage of these databases and tools, and how they relate to researchers in the field of energy generation and storage.
9:35 10 Sustainable chemistry in the CAS databases

Cristian Dumitrescu1, cdumistrescu@cas.org, Roger Schenck2. (1) Department of Marketing, Chemical Abstracts Service, Columbus, OH 43202, United States, (2) Department of Marketing, Chemical Abstracts Service, Columbus, OH 43202, United States

Covering chemistry in its broadest sense, the CAS databases are a reflection of the research efforts in the area of chemistry for environmental sustainability. From greener syntheses of pharmaceutical candidates, to more efficient conversion of the biomass, to new energy storage materials, this presentation will cover discovering insights into these technologies. In the area of planning greener synthetic procedures, a focus will be on finding more environmentally friendly catalysts and solvents in CAS's collection of chemical reactions.
10:05 Intermission
10:20 11 Fading shades of gray? ACS Meeting preprints past, present, and future

David Flaxbart, flaxbart@austin.utexas.edu, Mallet Chemistry Library, University of Texas at Austin, Austin, TX 78713, United States

Meeting preprints from the energy-related divisions of ACS have been a part of the disciplinary literature since the 1930s. But the march of time seems to be leaving them behind, and even access to the legacy content is under threat from several quarters. This presentation will offer a quick history of this unique format of gray literature, the present state of affairs, and some advice for the future.
10:50 12 On the fly collection development to support emergent energy research initiatives

Donna T. Wrublewski, dtwrublewski@library.caltech.edu, George Porter, Dana Roth. Sherman Fairchild Library, California Institute of Technology, Pasadena, CA 91125, United States

Within the last few years, two major energy research initiatives have been undertaken on the Caltech campus: the Resnick Sustainability Institute (RSI) and the Joint Center for Artifical Photosynthesis (JCAP). RSI's research includes the production of electricity and fuels from renewable sources, the distribution and storage of energy, and other sustainability projects. JCAP's area of research is focused on achieving a system of artificial photosynthesis for utilizing solar energy. Both of these projects require resources from a broad range of fields, including chemistry, physics, biology, environmental &systems engineering, and more. This talk will give a brief description of some of the research being done in these projects, along with an overview of where energy research has traditionally been categorized in terms of collection development. A publication analysis will be presented to elucidate where information is being referenced from and where affiliated researchers are publishing, and how this correlates with the current collection holdings. Other considerations, such as identifying resources, outreach to groups about availability, and re-use of the collections, will also be discussed.
11:20 13 X marks the spot: Using xSearch for discovering energy information

Grace Baysinger, graceb@stanford.edu, Swain Chemistry &Chemical Engineering Library, Stanford University, Stanford, CA 94305-5081, United States

Online collections in academic research libraries are growing at a rapid pace. To help users discover relevant information in the "digital stacks", robust yet intuitive discovery tools are needed. Multidisciplinary researchers in areas such as energy and the environment need to a broad array of resources to meet their information needs. xSearch is a locally customized federated search service that lets users search 250+ sources (databases, data &statistics, full-text books, full-text journals, grant &funding sources, government documents, images, streaming media, news, patents, reference materials, reports, and theses &dissertations). This presentation will cover energy-related resources selected for xSearch and will summarize search features available for finding relevant information.
11:50 Concluding Remarks

Sunday, March 16, 2014

Joint CINF-RSC CICAG Symposium: Chemical Schemas, Taxonomies and Ontologies - PM Session
Platforms and Processes

Omni Dallas Hotel
Room: Deep Ellum A
Cosponsored by COMP, MEDI, ORGN, PHYS
Leah McEwen, Antony Williams, Jeremy Frey, Simon Coles, Organizers
Jeremy Frey, Presiding
1:30 pm - 5:00 pm
1:30 Introductory Remarks
1:35 14 Building a semantic chemistry platform with the Royal Society of Chemistry

Valery Tkachenko, tkachenkov@rsc.org, Colin Batchelor, Peter Corbett, Antony Williams. eScience, Royal Society of Chemistry, Cambridge, Cambridgeshire CB4 0WF, United Kingdom

We live in an exponentially expanding world of “big data”. Social networks, global portals and other distributed systems have been attempting to deal with the problem for a few years now. Scientific applications are commonly lagging behind the mainstream trends due to the complexity of the scientific domain. The Royal Society of Chemistry is building the Global Chemistry Network connecting a variety of resources both in-house and external, bridging gaps and advancing the chemical sciences. One of the main issues connected to the world of big data is the ease of navigation and comprehensiveness of the search capabilities. This is where the approach of the semantic web meets the world of big data. We will present our approaches in building a global federated chemistry platform connecting multiple domains of chemistry using semantic web technologies.
2:00 15 Ontology work at the Royal Society of Chemistry

Antony J. Williams, williamsa@rsc.org, Colin Batchelor, Peter Corbett, Jon Steele, Valery Tkachenko. eScience, Royal Society of Chemistry, Cambridge, Cambridgeshire CB4 0WF, United Kingdom

We provide an overview of the use we make of ontologies at the Royal Society of Chemistry. Our engagement with the ontology community began in 2006 with preparations for Project Prospect, which used ChEBI and other Open Biomedical Ontologies to mark up journal articles. Subsequently Project Prospect has evolved into DERA (Digitally Enhancing the RSC Archive) and we have developed further ontologies for text markup, covering analytical methods and name reactions. Most recently we have been contributing to CHEMINF, an open-source cheminformatics ontology, as part of our work on disseminating calculated physicochemical properties of molecules via the Open PHACTS. We show how we represent these properties and how it can serve as a template for disseminating different sorts of chemical information.
2:25 16 PubChem: Data access, navigation, and integration by means of classifiers and ontologies

Evan Bolton, bolton@ncbi.nlm.nih.gov, National Center for Biotechnology Information, Bethesda, MD 20894, United States

PubChem is a sizeable archive of chemical biology information with over 115 million sample descriptions, 46 million unique small molecules, and 200 million biological activity results. Navigation of such a large corpus of information is made easier by the means of classification systems (such as NLM's MeSH and WIPO's IPC) and ontologies (such as EBI's ChEBI and Gene Ontology Consortium's GO). Coupled with semantic annotation provided by the PubChemRDF project, data integration is facilitated across scientific domains. This talk will demonstrate how classifiers and ontologies are leveraged within the PubChem resource to improve data navigation but also how chemical identity groups and similarity play a key role in locating related chemical information.
2:50 17 AMI2: High-through extraction of semantic chemistry from the scientific literature

Andy Howlett, aph36@cam.ac.uk, Mark Williamson, Peter Murray-Rust. Department of Chemistry, Unilever Centre for Molecular Informatics, University of Cambridge, Cambridge, United Kingdom

The OpenSource AMI2-chem system ingests the scientific literature and extracts chemical facts on a high-throughput basis. It can take a variety of inputs, most importantly PDF and images (e.g. PNG) and transform them successively into SVG, XHTML and finally CML (Chemical Markup Language). Chemistry can be extracted from text, tables and diagrams and represented as molecules, reactions, recipes/procedures (ChemicalTagger), spectra, classification trees and more generally plots and data tables. The text and tables are created in XHTML and SVG. Other AMI2 systems extract biological sequences, species and phylogenetics (NexML) so creating a multidisciplinary semantic resource.
3:15 Intermission
3:30 18 Creating context for the experiment record: User-defined metadata

Cerys Willoughby, cerys.willoughby@me.com, Jeremy G Frey, Simon J Coles, Colin L Bird. Department of Chemistry, University of Southampton, Southampton, Hampshire SO17 1BJ, United Kingdom

The drive towards more transparency in research and open data increases the importance of being able to find information and make links to the data. Metadata is an essential ingredient for facilitating discovery and is used in Electronic Laboratory Notebooks to curate experiment data and associated entries with descriptive information and classification labels that can be used for aggregation and identification. Machine-generated metadata helps with facilitating metadata exchange and enabling interoperability, but such metadata is not necessarily in a form friendly for the humans that also need it. A survey of metadata usage in an ELN developed at the University of Southampton indicates many users do not use metadata effectively. Whilst some groups are comfortable with metadata and are able to design a metadata structure that works effectively, many users have no knowledge of where to start to define metadata or even an understanding of what it is and why it is useful. The metadata used within the notebooks is dominated by a few categories, in particular materials, data formats, and instruments. Further investigation is under way to determine whether this pattern of metadata use is common in other online environments, whether users are more likely to create certain types of metadata, and whether lessons can be learned from other environments to encourage metadata use. These findings will contribute to strategies for encouraging and improving metadata use in ELNs such as improved interface designs, user education, standard schema designs, and encouraging collaboration between same-discipline groups to promote consistency and best practices.
3:55 19 Experiment markup langauge: A combined markup language and ontology to represent science

Stuart Chalk, schalk@unf.edu, Department of Chemistry, University of North Florida, Jacksonville, FL 32224, United States

In its basic essence, when we perform science we create a detailed journal of what we do. In order to capture this in the context of the semantic web it is necessary to break down the scientific process and look at the types of information that we record. The Experiment Markup Language (ExptML) is proposed as a framework for capturing the content and context of science experiments. This is coupled with an ontology that represents the relationships between content elements, thus creating a graph of science experiments. A discussion of the current version of this system will be presented with examples along with a roadmap of future development.
4:20 20 Development of formal representations of the synthesis and processing histories of metal-organic frameworks (MOFs) using the ChemAxiom, ChEBI, CMO, and CHEMINF ontologies

Nico Adams1, Nico.Adams@csiro.au, Danielle Kennedy1, Murray Jensen1, Cornelius Kloppers2, Yanfeng Shu2, Claire D'Este2, Craig Lindley2. (1) Materials Science and Engineering, CSIRO, Clayton, Victoria 3168, Australia, (2) Computational Informatics, CSIRO, Hobart, Tasmania 7001, Australia

Metalorganic frameworks – a subset of coordination polymers - are currently a hot topic in chemical and materials research. They have some of the highest recorded surface areas and are finding applications in gas storage, catalysis and biosensing areas. Significant repositories of both physical MOF collections and data about MOFs (whether experimentally determined or computed) are currently being assembled by the research community and informatics systems for the retrieval of appropriate information associated with these compounds are required. However, informatics issues associated with MOFs remain to be resolved. For example, there are currently no internationally accepted naming conventions or topology descriptions despite a first recommendation by IUPAC, which was recently published. The formal and ontology-driven representation of MOFs, their structural features as well as their synthetic histories, will go some way towards overcoming challenges in information retrieval associated with these compounds and may also facilitate greater MOF data interoperability and re-use. This talk will illustrate our approach to the development of such representations and will illustrate, how these representations can be leveraged in a number of application contexts.
4:45 Panel Discussion

Sunday, March 16, 2014

Translational Cancer Bioinformatics: Data, Methods and Applications - PM Session

Omni Dallas Hotel
Room: Deep Ellum B
Cosponsored by COMP

Rachelle Bienstock, Shuxing Zhang, Organizers
Shuxing Zhang, Presiding
1:00 pm - 3:00 pm
1:00 21 New chemistry and powerful interactive technologies to discover PPI antagonists

Carlos J. Camacho, ccamacho@pitt.edu, Computational and Systems Biology, University of Pittsburgh, Pittsburgh, PA 15260, United States

Although there is no shortage of potential protein-protein interaction (PPI) drug targets, only a handful of known low-molecular-weight inhibitors exist. One problem is that current efforts are dominated by low-yield high-throughput screening, whose rigid framework is not suitable for the diverse chemotypes present in PPIs. Here, I will describe recent progress in our efforts to develop open access interactive (i.e., real-time) web-based drug discovery technologies. Our goal is to bring knowledge into the virtual screening pipeline by developing tools that create synergy between chemist, biologist, and other experts to deliver (ant)-agonists for hard targets. The pharmacophore-based technologies build on the role of anchor residues, or deeply buried hot spots, have in molecular recognition of PPIs. Novel tera-chemistry that redesigns these entry points with anchor-biased virtual multicomponent reactions delivers tens of millions of readily synthesizable compounds. Application of this approach to the MDM2/p53 cancer target led to high hit rates, resulting in a large and diverse set of confirmed inhibitors, and co-crystal structures validate the design strategy. Our unique technologies promise to expand the development of novel chemical probes for cancer research and the exploration of the human interactome by leveraging in-house small-scale assays and user-friendly chemistry to rationally design ligands for PPIs with known structure.
1:30 22 Integrative analysis of multidimensional cancer genomics data

Shihua Zhang, Wenyuan Li, Chun-Chi Liu, X. Jasmine Zhou, xjzhouo@usc.edu. Molecular and Computational Biology, University of Southern California, Los Angeles, CA 90068, United States

Recent technology has made it possible to simultaneously perform multi-platform genomic profiling of biological samples, resulting in so-called 'multi-dimensional genomic data'. Such data provide unique opportunities to study the coordination between regulatory mechanisms on multiple levels. However, integrative analysis of multi-dimensional genomics data for the discovery of combinatorial patterns is currently lacking. Here, we develop several methods to address this challenge. We applied our methods to the multi-dimensional ovarian cancer data from the The Cancer Genome Atlas project, including the copy number variation, DNA methylation, gene expression and microRNA expression data. We successfully identified perturbed pathways that would have been overlooked with only a single type of data, uncovered associations between different layers of cellular activities and allowed the identification of clinically distinct patient subgroups. Our study provides useful protocols for uncovering hidden patterns and their biological implications in multi-dimensional 'omic' data.
2:00 23 New application to estimate the diversity of molecular databases

Iwona Weidlich1, iweidlic@coddes.com, Igor Filippov2. (1) CODDES LLC, Rockville, MD 20852, United States, (2) VIF Innovations LLC, Rockville, MD 20852, United States

To build a SAR/QSAR model applicable to a wide variety of chemotypes the training set should be diverse, but exactly how diverse and what is the appropriate measure of diversity is still an unresolved problem. Some of the frequently used ways to measure diversity include: a) Bio‑activity profile or distribution of physico-chemical properties b) Distribution or central moments of pairwise similarity c) Clustering-based approaches and dimension reduction. Bio-activity data and physico-chemical properties are not always available for all chemical structures of interest. Methods relying on mean pairwise similarity make an a priori assumption that the underlying distribution is of a specific shape (i.e. Gaussian), while methods using either clustering or a distribution of properties make it difficult to quantify to compare two very different sets of molecules to claim that one is more diverse than the other. Therefore we explored a possibility of creating a diversity measure which satisfies the following criteria: d) it is trivially computed from the structure itself for any structure, e) it is applicable to any set of molecules without any a priory assumptions about its composition f) it is easy to use to compare two different sets. With the increasing availability of large datasets of molecules numbering in tens of millions of structures there is enough publicly accessible data to conduct an investigation into the diversity distribution over a set of sets of randomly selected compounds which has not been possible before. We present a new application to estimate the diversity of a chemical set of molecules.
2:30 24 Computational analysis of pleckstrin homology (PH) domains for cancer drug development

Shuxing Zhang, shuxing@gmail.com, Department of Experimental Therapeutics, MD Anderson Cancer Center, Houston, TX 77054, United States

The pleckstrin homology (PH) domain is a protein domain of approximately 120 residues that occurs in a variety of proteins involved in intracellular signaling or as constituents of the cytoskeleton. Through interactions with phosphatidylinositol lipids and other proteins, PH domain plays a critical role in recruiting oncogene proteins (e.g., Akt) to the membranes for activation and thus contributing to cancer growth. In present study, we attempt to understand the PH domain structures and their genomics signatures which may help us design specific inhibitors for targeted cancer therapies. PH domains have low sequence identity, usually below 30%. To date over 30 PH domain structures have been determined. Upon analyzing these structure, it has been demonstrated that the 3D fold of PH domains is highly conserved, with a N-terminal α-helix, followed with seven β-strand structures. The loops connecting these β-strands can differ significantly in length, and this may provide the source of the domain's specificity. Indeed individual PH domains possess affinities and specificities for different phosphoinositides. Also based on our structural analysis, we implemented position-site specific matrices (PSSM), which have been used to determine the secondary structures for query sequences. Additionally we employed the phylogenic tree of PH domain constructed based upon the PSSM to classify the PH domain and our observations are in agreement to their known binding specificity to different phosphoinositides, and thereby allowing design of selective inhibitor binding. This strategy has been rigorously cross-validated with our PH domain structure data set, and it was also successfully applied to prediction of the GAB1 PH domain structure, followed by discovery of potent GAB1 inhibitors to kill cancer cells.

Sunday, March 16, 2014

Neglected and Rare Disease Drug Discovery Needs Open Data - PM Session

Omni Dallas Hotel
Room: Deep Ellum B

Antony Williams, Joel Freundlich, Sean Ekins, Organizers
Sean Ekins, Presiding
3:15 pm - 5:15 pm
3:15 25 Looking back at Mycobacterium tuberculosis mouse efficacy testing to move new drugs forward

Sean Ekins1,2, ekinssean@yahoo.com, Robert C Reynolds3, Antony J Williams4, Alex M Clark5, Joel S Freundlich6. (1) Collaborations in Chemistry, United States, (2) Collaborative Drug Discovery, inc, United States, (3) University of Alabama at Birmingham, United States, (4) Royal Society of Chemistry, United States, (5) Molecular Materials Informatics, Canada, (6) Rutgers University, United States

An urgent need exists to find new therapeutic options to address drug resistance and shorten therapy for those infected with Mycobacterium tuberculosis (Mtb). Whole-cell phenotypic screens have yielded well over 1500 in vitro inhibitors of Mtb which must be prioritized for in vivo testing. The mouse in vivo model for Mtb infection represents a validated model that is commonly utilized to select compounds for later studies. We have examined the data from the 1940's to the present day on this in vivo model which has not previously been curated. We have performed extensive structure-activity analysis and machine learning modeling that highlight new insights that could aid Mtb drug discovery. For example a Bayesian model (N = 338) had similar statistics to previously published in vitro models (ROC Score = 0.77, concordance = 70.57, specificity = 68.81 and sensitivity = 72.14). SVM and tree based models were also generated. We also describe how the SAR Table mobile app can be employed to mine local structure activity relationships. We will also describe the steps needed to make this open data.
3:45 26 Sharing methods to build predictive machine learning models for neglected and rare disease drug discovery

Paul J Kowalczyk, pauljkowalczyk@gmail.com, Department of Computational Chemistry, SCYNEXIS, Research Triangle Park, NC 27709-2878, United States

We present – and share - sets of 'better practices' for eight machine learning methods, focusing on classification: recursive partitioning, random forests, neural networks, partial least squares, support vector machines, k-nearest neighbors, self-organizing maps and naïve bayes. Various tuning parameters for each method are analyzed, e.g. the dimensions and topology of a self-organizing map; the depth of trees for partitioning methods; the number of nodes / hidden nodes in a neural network; the choice of kernel. The choice of molecular descriptors has also been studied. Descriptors studied include topological descriptors (e.g., atom pairs), circular fingerprints (e.g., ECFP / FCFP), and constitutive fingerprints (e.g., MDL keys). Metrics for model performance include AUC, sensitivity, specificity and Cohen's kappa. The success and utility of these 'better practices' are demonstrated using publicly available antimalarial datasets. Each data mining effort is collected into a compendium – an interactive document that bundles primary data, statistical methods, figures and derived data together with textual documentation and conclusions. This interactivity allows one to reproduce the research, and modify and extend the various components. We show how the compendia might be used for neglected and rare disease drug discovery and, additionally, how they might serve as tutorials for data mining. Specifically, we demonstrate how one might use the compendia to build predictive machine learning models for any dataset. The open-source R software environment is used for all data mining tasks. All text, code, data and auxiliary content will be made freely available.
4:15 27 Royal Society of Chemistry developments to support open drug discovery

Antony J. Williams, williamsa@rsc.org, Alexey Pshenichnov, Jon Steele, Ken Karapetyan, Richard Gay, Valery Tkachenko. eScience, Royal Society of Chemistry, Cambridge, Cambridgeshire CB4 0WF, United Kingdom

In recent years the Royal Society of Chemistry has become known for our development of freely accessible data platforms including ChemSpider, ChemSpider Reactions and our new chemistry data repository. In order to support drug discovery RSC participates in a number of projects including the Open PHACTS semantic web project, the PharmaSea natural products discovery project and the Open Source Drug Discovery project in collaboration with a team in India. Our most recent developments include extending our efforts to support neglected diseases by the provision of high quality datasets resulting from our curation efforts to support modeling, the delivery of enhanced application programming interfaces to allow open source drug discovery teams to both source and deposit data from our chemistry databases and the provision of a micropublishing platform to report on various aspects of work supporting neglected disease drug discovery. This presentation will review our existing efforts and our plans for extended development.
4:45 28 How can PubChem be leveraged for neglected and rare disease drug discovery?

Evan Bolton, bolton@ncbi.nlm.nih.gov, National Center for Biotechnology Information, Bethesda, MD 20894, United States

PubChem is a free resource serving the chemical biology community. PubChem contains more than 215 million biological test results from over 715 thousand biological experiments. This data covers nearly two million unique small molecules and six thousand unique defined protein targets. PubChem is an open archive and provides a platform for scientists to share data. PubChem integrates this information with other biomedical resources found at the U.S. National Center for Biotechnology Information, such as PubMed and GenBank. This talk will help show how PubChem can be harnessed by drug discovery researchers in their quest for cures of tropical, rare, and neglected and diseases (TRND).

Sunday, March 16, 2014

CINF Scholarship for Scientific Excellence - EVE Session

Omni Dallas Hotel
Room: Dallas C

Guenter Grethe, Organizers
, Presiding
6:30 pm - 8:30 pm

29 Efficacy of chemical hyperstructures in similarity searching and virtual screening

Edmund Duesbury, lip12ed@sheffield.ac.uk, John Holliday, Peter Willett. Information School, University of Sheffield, Sheffield, South Yorkshire S1 4DP, United Kingdom

Two techniques exist in data fusion which have been proven to work in various forms in chemoinformatics: similarity fusion, where different similarity measures are combined; and group fusion, where similarities are combined from multiple reference molecules. The hyperstructure concept however is another form of data fusion, being a hypothetical moleculethat is constructed from the overlap of a set of existing molecules. Initially proposed to reduce the time of database searching, it has also been used directly for virtual screening on two occasions since its inception [1,2], the latter of which showed it to be useful as a 2-dimensional QSAR method. The concept's performance however in 2-dimensional similarity searching has to date not been shown to be effective, and has not been evaluated thoroughly on large sets of compounds. The work being carried out in this project aims to evaluate hyperstructures as an alternative (if not superior) method for fusion-based similarity-searching, with an emphasis on virtual screening. Current progress on the project will be discussed, including a brief overview of how hyperstructures are constructed, evaluated for virtual screening and compared with existing search methods. Of particular interest will be a comparison with existing data fusion methods. Results in this work show that the hyperstructure concept is not as effective for virtual screening as group fusion using ECFP4 fingerprints in terms of numbers of actives retrieved, but retrieves a greater diversity of molecules. This suggests that the two approaches are complementary, suggesting that it may be beneficial to apply similarity fusion to the two techniques to improve virtual screening. References [1] Brown, N. PhD Thesis. University of Sheffield, 2002. [2] Palyulin, Radchenko, &Zefirov. (2000). Molecular field Topology analysis method in QSAR studies of organic compounds. J Chem. Inf. Comput. Sci, 40, 659–667.

30 3D-QSAR using quantum-mechanics-based molecular interaction fields

Ahmed El Kerdawy1, Ahmed.Elkerdawy@fau.de, Stefan Güssregen2, Hans Matter2, Matthias Hennemann1,3, Timothy Clark1,3,4. (1) Computer-Chemistry-Center, Friedrich-Alexander University Erlangen-Nürnberg, Erlangen, Germany, (2) R&D, LGCR, Structure, Design and Informatics, Sanofi-Aventis Deutschland GmbH, Frankfurt am Main, Germany, (3) Interdisciplinary Center for Molecular Materials, Friedrich-Alexander University Erlangen-Nürnberg, Erlangen, Germany, (4) Centre for Molecular Design, University of Portsmouth, Portsmouth, United Kingdom

The natural evolution of the different computer-aided drug design (CADD) methods involves a shift toward using quantum-mechanics (QM)-based approaches. This shift is not only the result of the ever growing computational power but also due to the need for more accurate and more informative approaches to describe molecular properties and binding characteristics than the currently available ones. QM approaches do not suffer from the limitations inherent to the ball-and-spring description and the fixed atom-centered charge approximation in the classical force fields mostly used by CADD methods. In this project we introduce a protocol for shifting 3D-QSAR, one of the most widely used ligand-based drug design approaches, through using QM based molecular interaction fields (MIFs) which are the electron density (ρ), hydrogen bond donor field (HDF), hydrogen bond acceptor field (HAF) and molecular lipophilicity potential (MLP) to overcome the limitations of the current force-field-based MIFs. The average performance of the QM-MIFs (QMFA) models for nine data sets was found to be better than that of the conventional force-field-based MIFs models. In the individual data sets, the QMFA models always perform better than, or as well as, the conventional approaches. It is particularly encouraging that the relative performance of the QMFA models improves in the external validation.


31 PoseView: Visualization of protein-ligand interactions in 2D

Katrin Stierand, stierand@zbh.uni-hamburg.de, Matthias Rarey. ZBH Center for Bioinformatics, University of Hamburg, Hamburg, Germany

Computational methods for drawing small molecules are well-established in chemistry and the associated scientific fields. For the 2D visualization of protein-ligand complexes there is considerably less choice. We developed PoseView, which generates two-dimensional diagrams of protein-ligand complexes, showing the ligand, the interactions and the interacting residues. All depicted molecules are drawn on an atomic level as structure diagrams; thus, the output plots are clearly structured and easily readable for the scientist. The algorithm is based on a combinatorial optimization strategy which solves parts of the layout problem non-heuristically. PoseView is widely accepted in the community: it is incorporated in the PDB providing a diagram for each protein with a co-crystallized druglike ligand. Large-scale application studies on approximately 200,000 complexes from the PDB reached success rates of > 92%. Beyond the depiction of single complex diagrams the comparative two-dimensional graphical representation of protein-ligand complex series featuring different ligands bound to the same active site offers a quick insight in their binding mode differences. In comparison to arbitrary orientations of the residue molecules in the individual complex depictions a consistent placement improves the legibility and comparability within the series. The automatic generation of such consistent layouts offers the possibility to apply it to large data sets originating from computer-aided drug design methods. We developed a new approach, which automatically generates a consistent layout of interacting residues for a given series of complexes. The method generates high-quality layouts, showing mostly overlap-free solutions with molecules which are displayed as structure diagrams providing interaction information in atomic detail. Compared to existing approaches these drawings substantially simplify the visual analysis of large compound series. In our contribution we will present an overview of the algorithms and an insight in the application of PoseView in different scenarios.

32 Metal template approach towards efficiency enhancement in hydrogen-bond promoted enantioselective organocatalysis

Tathagata Mukherjee, tathagata.mukherjee@chem.tamu.edu, John A. Gladysz. Department of Chemistry, Texas A&M University, College Station, Texas 77840, United States

The concept of preorganization involves engineering a receptor to be complementary to a guest prior to a binding event. This can render the host-guest interaction entropically and enthalpically more favorable. This notion can be extended further to chiral hydrogen bond donors as they are immensely popular in enantioselective organocatalysis. To put to test the effect of "metal-templated efficency enhancement in organocatalysis" we have chosen a 2-guanidinobenzimidazole derivative (GBI ) as a simple hydrogen bond donor. GBI upon complexation to transition metals becomes preorganized for several hydrogen bonding motifs. With preorganization, the rotational degrees of freedom that are intrinsic to the ligand are greatly reduced and both the reactivity and enantioselectivity are enhanced significantly.

The generality of the catalytic behavior was established by extending the Michael addition reaction to various dicarbonyls and different nitroolefins. Exceeding the expectation, the "ruthenium-templated" catalyst showed good enantioselectivity even in the cases of notoriously infamous (in terms of enantioselectivity) alkyl nitroolefins. The above results are self-evident enough to combine "organocatalysis" with "metal-templated efficiency enhancement" to support the title. These new class of hybrid (organic-inorganic) hydrogen bond donors is unique and has excellent potential to start up a new branch of catalysis.

Monday, March 17, 2014

Keeping the Thrill Alive: Research Data and Electronic Notebooks - AM Session
Data Curation

Omni Dallas Hotel
Room: Deep Ellum A
Cosponsored by COMP, MEDI, ORGN, PHYS
Antony Williams, Jeremy Frey, Simon Coles, Leah McEwen, Organizers
Antony Williams, Leah McEwen, Presiding
8:30 am - 11:50 am
8:30 Introductory Remarks
8:35 33 Profiling common types of research data produced by chemists at the University of Michigan

Ye Li, liye@umich.edu, Shapiro Science Library, University of Michigan, Ann Arbor, Michigan 48109, United States

Best practices in data management and metadata standards for Chemistry data are still mostly under development with the exception of areas related to mature “big data” fields such as geochemistry. In order to support data sharing in Chemistry research communities, our first step is to identify the common types of research data produced by Chemists. These different types of data can be grouped according to different research themes meaningful for a specific research community to form the Data Type Profile (DTP) of the research community. For example, for organic synthesis, its DTP can include chemical structures, reaction schemes, physical and chemical properties, spectral data, thermodynamic data of reactions, chromatographic data, and crystallographic data etc. and the specific types of data under these categories. The basic DTP can be enriched with relevant data lifecycle stories to form a comprehensive DTP and then be used to propose metadata standards and best practices in managing and sharing data. Here, as a case study, publications authored by principal investigators (PIs) in the Department of Chemistry at the University of Michigan were retrieved from Web of Science and grouped by PIs. Those journal articles published during the past two years were selected as the main reference set. The data originated from these labs and appeared in texts, tables, figures, captions, and supplements of the articles were identified, described and categorized. The descriptions were collected in a FileMaker database to be grouped under different research themes so that we could construct DTP for each research theme instead of traditional sub-discipllines. By completing DTP for the research themes in the Chemistry Department, we will obtain a representative scope of the common types of data to the interest of chemists and use it as the foundation to facilitate data sharing in Chemistry.
8:55 34 Distributing, managing, and updating cheminformatics experiments

Paul J Kowalczyk, pauljkowalczyk@gmail.com, Department of Computational Chemistry, SCYNEXIS, Research Triangle Park, NC 27709-2878, United States

We demonstrate how one might report cheminformatics experiments as instances of reproducible research, i.e., how one might author and distribute integrated dynamic documents that contain the text, code, data and any auxiliary content needed to recreate the computational results. We show how the contents of these documents, including figures and tables, can be recalculated each time the document is generated. This integration of computational code, method description and data allows researchers the opportunity to both verify the published research and adapt/extend the methods presented. Open-source tools are used for all document generation: the R software environment is used to process chemical structures and mine and analyze biological and chemical data; the knitr package is used to generate reports (PDF); the markdown package is used to generate valid (X)HTML content; and the beamer package is used to create slides for presentation. Specific examples are presented for the visualization, analysis and mining of publicly available antimalarial datasets, with particular attention paid to automatically generating PDF reports, slides for presentations and valid (X)HTML content. All text, code, data and auxiliary content will be made freely available.
9:15 35 Dark reaction project: Archiving and deriving value from unreported "failed" hydrothermal synthesis reactions

Joshua Schrier1, jschrier@haverford.edu, Sorelle Friedler2, Alexander Norquist1. (1) Department of Chemistry, Haverford College, Haverford, PA 19041, United States, (2) Department of Computer Science, Haverford College, Haverford, PA 19041, United States

Most chemical reactions that have been performed are deemed "unsuccessful" and are never reported in the literature. There is no forum for collecting these "dark reactions", nor a means for deriving value from them, but they are nevertheless valuable because they define the bounds on the reaction conditions needed to successfully synthesize a product. Moreover, this vast dataset is currently languishing in old laboratory notebooks. In this talk, we will describe our work on creating a searchable public online repository for reaction data that enables better management, sharing, and utilization of these dark reactions. Our initial efforts focus on the hydrothermal synthesis of organically-templated inorganic solids, as just a few reactants (one or two inorganic components, one or two organic components, and solvent) and a few reaction conditions (pH, temperature, reaction time) yield a diversity of products. We will describe the types of data we collect and the overall architecture of our database software. We will demonstrate the user interface for entering new reactions and searching existing reactions. We will discuss the potential for our (open-source) software to be adapted and utilized for other types of chemical synthesis data-management applications. Finally, we will describe our progress in using the "dark reaction" dataset to accelerate exploratory synthesis by using machine learning. We use cheminformatics software to compute derived properties of the reagents and trained a decision-tree algorithm to predict the success of new reactions. We then use this to perform virtual screening of commercially available reagents. We will discuss our preliminary results in experimentally validating these predictions.
9:35 36 Factors to consider when choosing the right ELN for capturing and collaborating with your research data

Philip Mounteney1, pm@dotmatics.com, Berkley A Lynch2, Tamsin E Mansley2, Sharang Phatak1, Jess W Sager1. (1) Dotmatics, Inc., San Diego, CA 92121, United States, (2) Dotmatics, Inc., Woburn, MA 01801, United States

Chemistry ELNs (electronic lab notebooks) have been evolving for years, and are becoming widely deployed. However, the structured format of the chemistry ELN does not satisfy the needs of other research groups. We will present a simple, easy-to-use, web-based electronic laboratory notebook that contains interfaces for chemists, biologists and other scientific disciplines in a fully compliant environment with audit trails. This is coupled with robust and flexible data searching capabilities that promote data sharing, collaboration, easy report generation and knowledge transfer. The web-based interface and cloud-based deployment described facilitate secure global and mobile access from a variety of devices in the lab, at the desk, across research/partner sites or on-the-go, particularly as the paradigm of BYOD (Bring Your Own Device) becomes more prevalent.
9:55 Intermission
10:10 37 Royal Society of Chemistry activities to develop a data repository for chemistry-specific data

Aileen Day, Alexey Pshenichnov, Ken Karapetyan, Colin Batchelor, Peter Corbett, Jon Steele, Valery Tkachenko, Antony J Williams, williamsa@rsc.org. eScience, Royal Society of Chemistry, Cambridge, United Kingdom

The Royal Society of Chemistry publishes many thousands of articles per year, the majority of these containing rich chemistry data that, in general, in limited in its value when isolated only to the HTML or PDF form of the articles commonly consumed by readers. RSC also has an archive of over 300,000 articles containing rich chemistry data especially in the form of chemicals, reactions, property data and analytical spectra. RSC is developing a platform integrating these various forms of chemistry data. The data will be aggregated both during the manuscript deposition process as well as the result of text-mining and extraction of data from across the RSC archive. This presentation will report on the development of the platform including our success in extracting compounds, reactions and spectral data from articles. We will also discuss our developing process for handling data at manuscript deposition and the integration and support of eLab Notebooks (ELNS) in terms of facilitating data deposition and sourcing data. Each of these processes is intended to ensure long-term access to research data with the intention of facilitating improved discovery.
10:30 38 Eureka research workbench: An open source eScience laboratory notebook

Stuart Chalk, schalk@unf.edu, Department of Chemistry, University of North Florida, Jacksonville, FL 32224, United States

Scientists are looking for ways to leverage web 2.0 technologies in the research laboratory and as a consequence a number of approaches to web-based electronic notebooks are being evaluated. In this presentation we discuss the Eureka Research Workbench, an electronic laboratory notebook built on semantic technology and XML. Using this approach the context of the information recorded in the laboratory can be captured and searched along with the data itself. A discussion of the current system is presented along with the development roadmap and long-term plans relative to linked open data.
10:50 39 PubChem: A platform to archive and share scientific information

Evan Bolton, bolton@ncbi.nlm.nih.gov, National Center for Biotechnology Information, Bethesda, MD 20894, United States

As an open archive, PubChem accepts substance sample descriptions, experimental results, textual annotations, and links to other on-line resources. PubChem incorporates and integrates data not only between contributors but also to the information content available at the US National Center for Biotechnology (NCBI), which includes PubMed and GenBank. In addition, PubChem provides a variety of tools to help researchers explore and analyze relevant information. This talk will help demonstrate how chemists can leverage the PubChem resource to archive and share their data with the community at large.
11:10 40 Keeping the thrill alive: Data on demand

Berkley A Lynch1, berkley.lynch@dotmatics.com, Tamsin E Mansley1, Philip Mounteney2, Sharang Phatak2, Jess W Sagar2. (1) Dotmatics, Inc., Woburn, MA 01801, United States, (2) Dotmatics, Inc., San Diego, CA 92121, United States

Continued access to research data after the original scientist has moved on, or after a project has wrapped up, is vital for any organization. This data is critical for publications or IP applications and yet it is often stored in disparate, sometimes inaccessible, places: e.g. a paper notebook on a PI's bookshelf, or multiple folders in scattered PC or network locations. Without guidance from the original scientist it is difficult to locate a specific piece of data. This situation is most prevalent in academic institutions where there is constant turnover of research staff, as students graduate and move on, as well as in short term industry partnerships with academia and CROs. We will present solutions that enable the secure and audited storage, retrieval, and sharing of data of all types between research partners, collaborators and customers, locally or across the globe. These solutions provide instant communication through the cloud or local network, enabling and enriching collaborative research, and providing continued access to original data long after the original researcher has moved on.
11:30 Panel Discussion

Monday, March 17, 2014

Keeping the Thrill Alive: Research Data and Electronic Notebooks - PM Session
eLab Notebooks

Omni Dallas Hotel
Room: Deep Ellum A
Cosponsored by COMP, MEDI, ORGN, PHYS
Leah McEwen, Antony Williams, Jeremy Frey, Simon Coles, Organizers
Simon Coles, Presiding
1:30 pm - 4:50 pm
1:30 Introductory Remarks
1:35 41 Building a mobile reaction lab notebook

Alex M Clark, aclark@molmatinf.com, R&D, Molecular Materials Informatics, Montreal, QC H3J2S1, Canada

Electronic Lab Notebook (ELN) software is a burgeoning field, with applicability to both industrial and academic research environments. Numerous products have been launched, tailored for large enterprises or small research groups. Many of these projects have an interface based on web technologies or native mobile apps. This presentation will describe the creation of a mobile interface specific to one major group of lab notebook users: synthetic chemists. A reaction-centric app can be designed to provide an effective user experience for specifying the scheme and experimental details of chemical reactions, and making them digitally available. By combining the user-facing mobile app with cloud-hosted algorithms and centralized databases, a large number of supporting features and reference data can be made available, and special attention will be paid to green chemistry metrics. The core technologies for this product have already been demonstrated in apps such as the Mobile Molecular DataSheet (MMDS), Reaction101, Yield101, MolSync and Green Solvents. The means by which these are assembled into a fully functional reaction lab notebook will be described.
1:55 42 Generating metadata for an experiment: Using a tablet ELN

Cerys Willoughby, cerys.willoughby@me.com, Jeremy G Frey, Simon J Coles, Susanne Coles. Department of Chemistry, University of Southampton, Southampton, Hampshire SO17 1BJ, United Kingdom

The drive towards more transparency in research and open data increases the importance of being able to find information and make links to the data. Metadata is an essential ingredient for facilitating this discovery. We have discovered from our analysis of metadata usage in the LabTrove ELN that many users do not use metadata effectively and in many cases do not understand what it is or why it is useful. LabTrove provides a flexible metadata framework, enabling the creation of two different kinds of user-defined metadata: Sections used to describe the content of the entries, and key-value pair data useful for describing specific elements of the experiment. When we developed a prototype tablet ELN called Notelus, able to integrate with LabTrove, we wanted to ensure that we could make the best use of the metadata capabilities of LabTrove by providing the users with the opportunity to add useful metadata simply and easily. Part of the decision making process for the development of Notelus was defining structures to represent an experiment and an associated plan based upon our experiences of how researchers planned, recorded, and organized their experiment data. Metadata is then automatically generated based on information provided by the user about the experiment and from the experiment plan if one is used in addition to basic metadata, such as author, date and time of creation, and name of the notebook. The result is metadata associated with the experiment record in LabTrove that represent the kinds of information that researchers use and search for, but including information that they have typically not considered using when they have created their own metadata manually.
2:15 43 Mining ELN based structured test and chemical property data to optimize catalyst development

Philip J Skinner, philip.skinner@perkinelmer.com, Joshua A Bishop, Josh.Bishop@PERKINELMER.COM, Rudy Potenzone, Megean Schoenberg. PerkinElmer, Waltham, Massachusetts 02451, United States

Understanding the relationship between chemical structure, chemical properties and assays was once the purview of lifesciences where systems and workflows have been developed to manage the flow of information and to inform decisions. Industrial chemists deal with fewer unique materials but are now equally interested in the correlation of material and the structured numerical results within tests and assays. Optimizing the physical performance of the materials is achieved through composition changes and measured through particle size distributions, rheological assays and other tests.
This presentation will present the outcome of a series of proof of concepts towards the optimization of chemical catalysts. In these examples the ELN was utilized, above and beyond a traditional record keeping role, to standardize the collection of structured numerical test data. In each case the correlated multi-test data was available for interrogation through Spotfire in order to optimize the physical characteristics of the material.
2:35 44 Sample management with the LabTrove ELN

Jeremy G Frey, j.g.frey@soton.ac.uk, Simon J Coles, Andrew J Milsted, Cerys Willoughby, Colin L Bird. Chemistry, University of Southampton, Southampton, Hampshire SO17 1BJ, United Kingdom

A significant advantage of the Electronic Laboratory Notebook (ELN) over its more traditional rival, the paper notebook, is the ability of the ELN to retain the journal characteristics of traditional notebooks while exploiting the potential for linking together procedures, materials, samples, observations, data, and analysis reports. The ability to link individual experiment records with the materials and samples used is particularly important for establishing unequivocally the provenance of a given procedure. Similarly, information relating to an instrument used to make critical measurements might also be a significant aspect of the provenance chain. LabTrove, a web-based ELN developed at the University of Southampton, provides a range of higher-level linking options that maintain the relationships between notebook entries and data objects. We report case studies that illustrate the application of the high-level linking features of LabTrove to sample management:[ul][li]Keeping track of separate samples and demonstrating reproducibility between batches of sample;[/li][li]Maintaining links between samples, experiment data, derived data, and subsequent publications;[/li][li]Using a combination of URI and barcodes to provide both ready identification of specific items and a simple sample management system, with no additional effort.[/li][/ul]
2:55 Intermission
3:10 45 Digital data repositories in chemistry and their integration with journals and electronic laboratory notebooks

Henry S Rzepa, rzepa@ic.ac.uk, Matt S Harvey, Nick Mason. Chemistry, Imperial College London, London, London SW 2AZ, United Kingdom

A web-based electronic laboratory notebook system for organising and conducting computational experiments and associated experimental data is described. This system manages the lifecycle of an experiment from instantiation, through execution on high-performance computing resources, to data retrieval and deposition of final results and metadata in a digital repository for long-term curation. We demonstrate integration with three different third-party repositories (SPECTRa-DSpace, Figshare and Chempound). Each of these provide citable access to their contents using persistent identifiers, following the principles of the Amsterdam Manifesto on data citation. Examples illustrating the two-publisher model of the scientific article are presented, in which the data object is cited via its persistent identifier (DOI) and presented as either a fileset or an interactive rendering of the data and transcluded into the narrative component of a publication. We demonstrate recent advances in our use of Handle identifiers (the underlying infrastructure of the DOI system) to expose dataset metadata using specific handle types, in conjunction with web service resolution of Handles/DOIs to structured data. This allows automated discovery and mining of datasets and thus enables, for example, the dynamic generation of complex, interactive views that could be integrated within e-lab notebooks.
3:30 46 Data exchange between electronic lab notebooks and data repositories

Rory Macneil, rmacneil@researchspace.com, Research Space, Edinburgh, United Kingdom
3:50 47 Standardized representations of ELN reactions for categorization and duplicate/variation identification

Roger A Sayle, roger@nextmovesoftware.com, Daniel M Lowe. NextMove Software, Cambridge, United Kingdom

Electronic lab notebooks (ELNs) can be considered experiment or document centric databases, where each record corresponds to a unique experiment. In an ELN, there is no intrinsic notion of a "duplicate", each experiment is represented by its own notebook page. Registration systems and more traditional reaction databases, on the other hand, are connection table centric, with duplicates identified and unique items assigned their own identifier or key. Populating reaction databases from (pharmaceutical) ELNs therefore requires an operational definition of "same reaction". Here we describe approaches and challenges to identifying reaction "variations" in large reaction databases. Amongst the techniques considered, is the use of the proposed IUPAC reaction InChI identifier or RInChI.
4:10 48 Extracting data, information, and knowledge from an ELN

Colin L Bird1, colinl.bird@soton.ac.uk, Simon J Coles1, Jeremy G Frey1, Richard J Whitby1, Aileen E Day2. (1) Chemistry, University of Southampton, Southampton, Hampshire SO17 1BJ, United Kingdom, (2) Royal Society of Chemistry, Cambridge, Cambridgeshire CB4 0WF, United Kingdom

Electronic Laboratory Notebooks (ELNs) are used routinely to capture and preserve procedures, materials, samples, observations, data, and analysis reports. ELNs also retain the journal characteristics of traditional paper notebooks, thus enabling the capture of thoughts and deliberations. ELNs contain a wealth of data, information, and knowledge that is organised internally but is not necessarily readily accessible for external reuse. Dial-a-Molecule is a UK Grand Challenge Network that promotes research aimed at bringing about a step change in our ability to deliver molecules quickly and efficiently: How can we make molecules in days not years? To realise this vision, it will be essential to exploit the vast body of currently inaccessible chemical data and information held in ELNs, not only to make that data and information available but also to develop protocols for discovery, access and ultimately automatic processing. The data-information-knowledge-wisdom (DIKW) hierarchy is often represented as a pyramid, with data at the base. Identifying relationships places data “in formation” and patterns lead to “actionable information”, which we usually think of as knowledge. We report research that uses the knowledge layer as the entry point to the DIKW pyramid as embodied within ELNs. Core metadata identifying the material being made available and how it might be obtained is published as an elnItemManifest, which is an XML file. If the material is potentially useful, another team can use the contact information in the elnItemManifest to obtain fuller contextual information – data “in formation” - held within the ELN. To reuse the material, the other team would request the detail metadata that describes the data itself. The Dial-a-Molecule approach regards this detail as the third layer of a three-tier model that corresponds to the DIKW hierarchy. If the vision is realised, chemists will have acquired the wisdom to make molecules in days not years.
4:30 Panel Discussion

Monday, March 17, 2014

Sci-Mix - EVE Session

Dallas Convention Center
Room: Hall F

Jeremy Garritano, Erin Bolstad, Organizers
, Presiding
8:00 pm - 10:00 pm

2 Ontology-driven information system for chemical and materials science

Nico Adams1, nico.adams@csiro.au, Murray Jensen1, Danielle Kennedy1, Cornelius Kloppers2, Yanfeng Shu2, Claire D'Este2, Craig Lindley2. (1) Materials Science and Engineering, CSIRO, Clayton, Victoria 3150, Australia, (2) Computational Informatics, CSIRO, Hobart, Tasmania 7001, Australia

Standard information systems for the chemical and materials sciences are almost entirely predicated on the notion of chemical structure and composition as the unique criterion of identity, which also encodes properties. However, the properties of many extended materials, such as polymers (including coordination polymers) are not comprehensible on the basis of their chemical structure and composition alone – rather they are often determined by the provenance and processing history of a material. The melting points of polymers, for example, can be significantly changed through a simple post-processing step such as compounding – this changes property-determining intermolecular interactions rather than fundamental chemistry and as such is not encoded by simple structure representations. This, in turn, means that chemical and process descriptions need to be interoperable and associable with chemical objects. Ontologies map particularly well onto the problem of developing integrated chemical and process representation of entities and can be used to develop complete provenance traces of materials. In this talk, we will discuss our approach to developing such representations and how they can be leveraged for multiple purposes in materials information systems.

8 Trends in bio-based chemicals: Business intelligence from published literature

Steve M Watson, s.watson@elsevier.com, Alternative Energy, Elsevier, Amsterdam, North Holland 1043NX, The Netherlands

A new information solution, Elsevier Biofuel, has been used to review the literature landscape, revealing trends in R&D towards the production of valuable chemicals from biomass. Elsevier Biofuel comprises advanced search and analysis tools, using a domain specific taxonomy to automatically classify over 21 million documents, many in full text, covering relevant journal publications, patents, technical reports, conference proceedings and trade publications. The analysis highlights emerging technology areas, commercial opportunities, and the leading companies staking a claim to this space.

18 Creating context for the experiment record: User-defined metadata

Cerys Willoughby, cerys.willoughby@me.com, Jeremy G Frey, Simon J Coles, Colin L Bird. Department of Chemistry, University of Southampton, Southampton, Hampshire SO17 1BJ, United Kingdom

The drive towards more transparency in research and open data increases the importance of being able to find information and make links to the data. Metadata is an essential ingredient for facilitating discovery and is used in Electronic Laboratory Notebooks to curate experiment data and associated entries with descriptive information and classification labels that can be used for aggregation and identification. Machine-generated metadata helps with facilitating metadata exchange and enabling interoperability, but such metadata is not necessarily in a form friendly for the humans that also need it. A survey of metadata usage in an ELN developed at the University of Southampton indicates many users do not use metadata effectively. Whilst some groups are comfortable with metadata and are able to design a metadata structure that works effectively, many users have no knowledge of where to start to define metadata or even an understanding of what it is and why it is useful. The metadata used within the notebooks is dominated by a few categories, in particular materials, data formats, and instruments. Further investigation is under way to determine whether this pattern of metadata use is common in other online environments, whether users are more likely to create certain types of metadata, and whether lessons can be learned from other environments to encourage metadata use. These findings will contribute to strategies for encouraging and improving metadata use in ELNs such as improved interface designs, user education, standard schema designs, and encouraging collaboration between same-discipline groups to promote consistency and best practices.

20 Development of formal representations of the synthesis and processing histories of metal-organic frameworks (MOFs) using the ChemAxiom, ChEBI, CMO, and CHEMINF ontologies

Nico Adams1, Nico.Adams@csiro.au, Danielle Kennedy1, Murray Jensen1, Cornelius Kloppers2, Yanfeng Shu2, Claire D'Este2, Craig Lindley2. (1) Materials Science and Engineering, CSIRO, Clayton, Victoria 3168, Australia, (2) Computational Informatics, CSIRO, Hobart, Tasmania 7001, Australia

Metalorganic frameworks – a subset of coordination polymers - are currently a hot topic in chemical and materials research. They have some of the highest recorded surface areas and are finding applications in gas storage, catalysis and biosensing areas. Significant repositories of both physical MOF collections and data about MOFs (whether experimentally determined or computed) are currently being assembled by the research community and informatics systems for the retrieval of appropriate information associated with these compounds are required. However, informatics issues associated with MOFs remain to be resolved. For example, there are currently no internationally accepted naming conventions or topology descriptions despite a first recommendation by IUPAC, which was recently published. The formal and ontology-driven representation of MOFs, their structural features as well as their synthetic histories, will go some way towards overcoming challenges in information retrieval associated with these compounds and may also facilitate greater MOF data interoperability and re-use. This talk will illustrate our approach to the development of such representations and will illustrate, how these representations can be leveraged in a number of application contexts.

21 New chemistry and powerful interactive technologies to discover PPI antagonists

Carlos J. Camacho, ccamacho@pitt.edu, Computational and Systems Biology, University of Pittsburgh, Pittsburgh, PA 15260, United States

Although there is no shortage of potential protein-protein interaction (PPI) drug targets, only a handful of known low-molecular-weight inhibitors exist. One problem is that current efforts are dominated by low-yield high-throughput screening, whose rigid framework is not suitable for the diverse chemotypes present in PPIs. Here, I will describe recent progress in our efforts to develop open access interactive (i.e., real-time) web-based drug discovery technologies. Our goal is to bring knowledge into the virtual screening pipeline by developing tools that create synergy between chemist, biologist, and other experts to deliver (ant)-agonists for hard targets. The pharmacophore-based technologies build on the role of anchor residues, or deeply buried hot spots, have in molecular recognition of PPIs. Novel tera-chemistry that redesigns these entry points with anchor-biased virtual multicomponent reactions delivers tens of millions of readily synthesizable compounds. Application of this approach to the MDM2/p53 cancer target led to high hit rates, resulting in a large and diverse set of confirmed inhibitors, and co-crystal structures validate the design strategy. Our unique technologies promise to expand the development of novel chemical probes for cancer research and the exploration of the human interactome by leveraging in-house small-scale assays and user-friendly chemistry to rationally design ligands for PPIs with known structure.

24 Computational analysis of pleckstrin homology (PH) domains for cancer drug development

Shuxing Zhang, shuxing@gmail.com, Department of Experimental Therapeutics, MD Anderson Cancer Center, Houston, TX 77054, United States

The pleckstrin homology (PH) domain is a protein domain of approximately 120 residues that occurs in a variety of proteins involved in intracellular signaling or as constituents of the cytoskeleton. Through interactions with phosphatidylinositol lipids and other proteins, PH domain plays a critical role in recruiting oncogene proteins (e.g., Akt) to the membranes for activation and thus contributing to cancer growth. In present study, we attempt to understand the PH domain structures and their genomics signatures which may help us design specific inhibitors for targeted cancer therapies. PH domains have low sequence identity, usually below 30%. To date over 30 PH domain structures have been determined. Upon analyzing these structure, it has been demonstrated that the 3D fold of PH domains is highly conserved, with a N-terminal α-helix, followed with seven β-strand structures. The loops connecting these β-strands can differ significantly in length, and this may provide the source of the domain's specificity. Indeed individual PH domains possess affinities and specificities for different phosphoinositides. Also based on our structural analysis, we implemented position-site specific matrices (PSSM), which have been used to determine the secondary structures for query sequences. Additionally we employed the phylogenic tree of PH domain constructed based upon the PSSM to classify the PH domain and our observations are in agreement to their known binding specificity to different phosphoinositides, and thereby allowing design of selective inhibitor binding. This strategy has been rigorously cross-validated with our PH domain structure data set, and it was also successfully applied to prediction of the GAB1 PH domain structure, followed by discovery of potent GAB1 inhibitors to kill cancer cells.

26 Sharing methods to build predictive machine learning models for neglected and rare disease drug discovery

Paul J Kowalczyk, pauljkowalczyk@gmail.com, Department of Computational Chemistry, SCYNEXIS, Research Triangle Park, NC 27709-2878, United States

We present – and share - sets of 'better practices' for eight machine learning methods, focusing on classification: recursive partitioning, random forests, neural networks, partial least squares, support vector machines, k-nearest neighbors, self-organizing maps and naïve bayes. Various tuning parameters for each method are analyzed, e.g. the dimensions and topology of a self-organizing map; the depth of trees for partitioning methods; the number of nodes / hidden nodes in a neural network; the choice of kernel. The choice of molecular descriptors has also been studied. Descriptors studied include topological descriptors (e.g., atom pairs), circular fingerprints (e.g., ECFP / FCFP), and constitutive fingerprints (e.g., MDL keys). Metrics for model performance include AUC, sensitivity, specificity and Cohen's kappa. The success and utility of these 'better practices' are demonstrated using publicly available antimalarial datasets. Each data mining effort is collected into a compendium – an interactive document that bundles primary data, statistical methods, figures and derived data together with textual documentation and conclusions. This interactivity allows one to reproduce the research, and modify and extend the various components. We show how the compendia might be used for neglected and rare disease drug discovery and, additionally, how they might serve as tutorials for data mining. Specifically, we demonstrate how one might use the compendia to build predictive machine learning models for any dataset. The open-source R software environment is used for all data mining tasks. All text, code, data and auxiliary content will be made freely available.

29 Efficacy of chemical hyperstructures in similarity searching and virtual screening

Edmund Duesbury, lip12ed@sheffield.ac.uk, John Holliday, Peter Willett. Information School, University of Sheffield, Sheffield, South Yorkshire S1 4DP, United Kingdom

Two techniques exist in data fusion which have been proven to work in various forms in chemoinformatics: similarity fusion, where different similarity measures are combined; and group fusion, where similarities are combined from multiple reference molecules. The hyperstructure concept however is another form of data fusion, being a hypothetical moleculethat is constructed from the overlap of a set of existing molecules. Initially proposed to reduce the time of database searching, it has also been used directly for virtual screening on two occasions since its inception [1,2], the latter of which showed it to be useful as a 2-dimensional QSAR method. The concept's performance however in 2-dimensional similarity searching has to date not been shown to be effective, and has not been evaluated thoroughly on large sets of compounds. The work being carried out in this project aims to evaluate hyperstructures as an alternative (if not superior) method for fusion-based similarity-searching, with an emphasis on virtual screening. Current progress on the project will be discussed, including a brief overview of how hyperstructures are constructed, evaluated for virtual screening and compared with existing search methods. Of particular interest will be a comparison with existing data fusion methods. Results in this work show that the hyperstructure concept is not as effective for virtual screening as group fusion using ECFP4 fingerprints in terms of numbers of actives retrieved, but retrieves a greater diversity of molecules. This suggests that the two approaches are complementary, suggesting that it may be beneficial to apply similarity fusion to the two techniques to improve virtual screening. References [1] Brown, N. PhD Thesis. University of Sheffield, 2002. [2] Palyulin, Radchenko, &Zefirov. (2000). Molecular field Topology analysis method in QSAR studies of organic compounds. J Chem. Inf. Comput. Sci, 40, 659–667.

30 3D-QSAR using quantum-mechanics-based molecular interaction fields

Ahmed El Kerdawy1, Ahmed.Elkerdawy@fau.de, Stefan Güssregen2, Hans Matter2, Matthias Hennemann1,3, Timothy Clark1,3,4. (1) Computer-Chemistry-Center, Friedrich-Alexander University Erlangen-Nürnberg, Erlangen, Germany, (2) R&D, LGCR, Structure, Design and Informatics, Sanofi-Aventis Deutschland GmbH, Frankfurt am Main, Germany, (3) Interdisciplinary Center for Molecular Materials, Friedrich-Alexander University Erlangen-Nürnberg, Erlangen, Germany, (4) Centre for Molecular Design, University of Portsmouth, Portsmouth, United Kingdom

The natural evolution of the different computer-aided drug design (CADD) methods involves a shift toward using quantum-mechanics (QM)-based approaches. This shift is not only the result of the ever growing computational power but also due to the need for more accurate and more informative approaches to describe molecular properties and binding characteristics than the currently available ones. QM approaches do not suffer from the limitations inherent to the ball-and-spring description and the fixed atom-centered charge approximation in the classical force fields mostly used by CADD methods. In this project we introduce a protocol for shifting 3D-QSAR, one of the most widely used ligand-based drug design approaches, through using QM based molecular interaction fields (MIFs) which are the electron density (ρ), hydrogen bond donor field (HDF), hydrogen bond acceptor field (HAF) and molecular lipophilicity potential (MLP) to overcome the limitations of the current force-field-based MIFs. The average performance of the QM-MIFs (QMFA) models for nine data sets was found to be better than that of the conventional force-field-based MIFs models. In the individual data sets, the QMFA models always perform better than, or as well as, the conventional approaches. It is particularly encouraging that the relative performance of the QMFA models improves in the external validation.


32 Metal template approach towards efficiency enhancement in hydrogen-bond promoted enantioselective organocatalysis

Tathagata Mukherjee, tathagata.mukherjee@chem.tamu.edu, John A. Gladysz. Department of Chemistry, Texas A&M University, College Station, Texas 77840, United States

The concept of preorganization involves engineering a receptor to be complementary to a guest prior to a binding event. This can render the host-guest interaction entropically and enthalpically more favorable. This notion can be extended further to chiral hydrogen bond donors as they are immensely popular in enantioselective organocatalysis. To put to test the effect of "metal-templated efficency enhancement in organocatalysis" we have chosen a 2-guanidinobenzimidazole derivative (GBI ) as a simple hydrogen bond donor. GBI upon complexation to transition metals becomes preorganized for several hydrogen bonding motifs. With preorganization, the rotational degrees of freedom that are intrinsic to the ligand are greatly reduced and both the reactivity and enantioselectivity are enhanced significantly.

The generality of the catalytic behavior was established by extending the Michael addition reaction to various dicarbonyls and different nitroolefins. Exceeding the expectation, the "ruthenium-templated" catalyst showed good enantioselectivity even in the cases of notoriously infamous (in terms of enantioselectivity) alkyl nitroolefins. The above results are self-evident enough to combine "organocatalysis" with "metal-templated efficiency enhancement" to support the title. These new class of hybrid (organic-inorganic) hydrogen bond donors is unique and has excellent potential to start up a new branch of catalysis.

33 Profiling common types of research data produced by chemists at the University of Michigan

Ye Li, liye@umich.edu, Shapiro Science Library, University of Michigan, Ann Arbor, Michigan 48109, United States

Best practices in data management and metadata standards for Chemistry data are still mostly under development with the exception of areas related to mature “big data” fields such as geochemistry. In order to support data sharing in Chemistry research communities, our first step is to identify the common types of research data produced by Chemists. These different types of data can be grouped according to different research themes meaningful for a specific research community to form the Data Type Profile (DTP) of the research community. For example, for organic synthesis, its DTP can include chemical structures, reaction schemes, physical and chemical properties, spectral data, thermodynamic data of reactions, chromatographic data, and crystallographic data etc. and the specific types of data under these categories. The basic DTP can be enriched with relevant data lifecycle stories to form a comprehensive DTP and then be used to propose metadata standards and best practices in managing and sharing data. Here, as a case study, publications authored by principal investigators (PIs) in the Department of Chemistry at the University of Michigan were retrieved from Web of Science and grouped by PIs. Those journal articles published during the past two years were selected as the main reference set. The data originated from these labs and appeared in texts, tables, figures, captions, and supplements of the articles were identified, described and categorized. The descriptions were collected in a FileMaker database to be grouped under different research themes so that we could construct DTP for each research theme instead of traditional sub-discipllines. By completing DTP for the research themes in the Chemistry Department, we will obtain a representative scope of the common types of data to the interest of chemists and use it as the foundation to facilitate data sharing in Chemistry.

34 Distributing, managing, and updating cheminformatics experiments

Paul J Kowalczyk, pauljkowalczyk@gmail.com, Department of Computational Chemistry, SCYNEXIS, Research Triangle Park, NC 27709-2878, United States

We demonstrate how one might report cheminformatics experiments as instances of reproducible research, i.e., how one might author and distribute integrated dynamic documents that contain the text, code, data and any auxiliary content needed to recreate the computational results. We show how the contents of these documents, including figures and tables, can be recalculated each time the document is generated. This integration of computational code, method description and data allows researchers the opportunity to both verify the published research and adapt/extend the methods presented. Open-source tools are used for all document generation: the R software environment is used to process chemical structures and mine and analyze biological and chemical data; the knitr package is used to generate reports (PDF); the markdown package is used to generate valid (X)HTML content; and the beamer package is used to create slides for presentation. Specific examples are presented for the visualization, analysis and mining of publicly available antimalarial datasets, with particular attention paid to automatically generating PDF reports, slides for presentations and valid (X)HTML content. All text, code, data and auxiliary content will be made freely available.

35 Dark reaction project: Archiving and deriving value from unreported "failed" hydrothermal synthesis reactions

Joshua Schrier1, jschrier@haverford.edu, Sorelle Friedler2, Alexander Norquist1. (1) Department of Chemistry, Haverford College, Haverford, PA 19041, United States, (2) Department of Computer Science, Haverford College, Haverford, PA 19041, United States

Most chemical reactions that have been performed are deemed "unsuccessful" and are never reported in the literature. There is no forum for collecting these "dark reactions", nor a means for deriving value from them, but they are nevertheless valuable because they define the bounds on the reaction conditions needed to successfully synthesize a product. Moreover, this vast dataset is currently languishing in old laboratory notebooks. In this talk, we will describe our work on creating a searchable public online repository for reaction data that enables better management, sharing, and utilization of these dark reactions. Our initial efforts focus on the hydrothermal synthesis of organically-templated inorganic solids, as just a few reactants (one or two inorganic components, one or two organic components, and solvent) and a few reaction conditions (pH, temperature, reaction time) yield a diversity of products. We will describe the types of data we collect and the overall architecture of our database software. We will demonstrate the user interface for entering new reactions and searching existing reactions. We will discuss the potential for our (open-source) software to be adapted and utilized for other types of chemical synthesis data-management applications. Finally, we will describe our progress in using the "dark reaction" dataset to accelerate exploratory synthesis by using machine learning. We use cheminformatics software to compute derived properties of the reagents and trained a decision-tree algorithm to predict the success of new reactions. We then use this to perform virtual screening of commercially available reagents. We will discuss our preliminary results in experimentally validating these predictions.

36 Factors to consider when choosing the right ELN for capturing and collaborating with your research data

Philip Mounteney1, pm@dotmatics.com, Berkley A Lynch2, Tamsin E Mansley2, Sharang Phatak1, Jess W Sager1. (1) Dotmatics, Inc., San Diego, CA 92121, United States, (2) Dotmatics, Inc., Woburn, MA 01801, United States

Chemistry ELNs (electronic lab notebooks) have been evolving for years, and are becoming widely deployed. However, the structured format of the chemistry ELN does not satisfy the needs of other research groups. We will present a simple, easy-to-use, web-based electronic laboratory notebook that contains interfaces for chemists, biologists and other scientific disciplines in a fully compliant environment with audit trails. This is coupled with robust and flexible data searching capabilities that promote data sharing, collaboration, easy report generation and knowledge transfer. The web-based interface and cloud-based deployment described facilitate secure global and mobile access from a variety of devices in the lab, at the desk, across research/partner sites or on-the-go, particularly as the paradigm of BYOD (Bring Your Own Device) becomes more prevalent.

40 Keeping the thrill alive: Data on demand

Berkley A Lynch1, berkley.lynch@dotmatics.com, Tamsin E Mansley1, Philip Mounteney2, Sharang Phatak2, Jess W Sagar2. (1) Dotmatics, Inc., Woburn, MA 01801, United States, (2) Dotmatics, Inc., San Diego, CA 92121, United States

Continued access to research data after the original scientist has moved on, or after a project has wrapped up, is vital for any organization. This data is critical for publications or IP applications and yet it is often stored in disparate, sometimes inaccessible, places: e.g. a paper notebook on a PI's bookshelf, or multiple folders in scattered PC or network locations. Without guidance from the original scientist it is difficult to locate a specific piece of data. This situation is most prevalent in academic institutions where there is constant turnover of research staff, as students graduate and move on, as well as in short term industry partnerships with academia and CROs. We will present solutions that enable the secure and audited storage, retrieval, and sharing of data of all types between research partners, collaborators and customers, locally or across the globe. These solutions provide instant communication through the cloud or local network, enabling and enriching collaborative research, and providing continued access to original data long after the original researcher has moved on.

42 Generating metadata for an experiment: Using a tablet ELN

Cerys Willoughby, cerys.willoughby@me.com, Jeremy G Frey, Simon J Coles, Susanne Coles. Department of Chemistry, University of Southampton, Southampton, Hampshire SO17 1BJ, United Kingdom

The drive towards more transparency in research and open data increases the importance of being able to find information and make links to the data. Metadata is an essential ingredient for facilitating this discovery. We have discovered from our analysis of metadata usage in the LabTrove ELN that many users do not use metadata effectively and in many cases do not understand what it is or why it is useful. LabTrove provides a flexible metadata framework, enabling the creation of two different kinds of user-defined metadata: Sections used to describe the content of the entries, and key-value pair data useful for describing specific elements of the experiment. When we developed a prototype tablet ELN called Notelus, able to integrate with LabTrove, we wanted to ensure that we could make the best use of the metadata capabilities of LabTrove by providing the users with the opportunity to add useful metadata simply and easily. Part of the decision making process for the development of Notelus was defining structures to represent an experiment and an associated plan based upon our experiences of how researchers planned, recorded, and organized their experiment data. Metadata is then automatically generated based on information provided by the user about the experiment and from the experiment plan if one is used in addition to basic metadata, such as author, date and time of creation, and name of the notebook. The result is metadata associated with the experiment record in LabTrove that represent the kinds of information that researchers use and search for, but including information that they have typically not considered using when they have created their own metadata manually.

46 Data exchange between electronic lab notebooks and data repositories

Rory Macneil, rmacneil@researchspace.com, Research Space, Edinburgh, United Kingdom

49 Stepping through virtual communication into Virtmon

Gwendolyn Tennell1,2, gtennell3669@skymail.susla.edu, Feng Li2. (1) Computer Science, Southern University Shreveport, Sheveport, Louisiana 71107, United States, (2) Computer Information and Graphics Technology, Indiana University Purdue University Indianapolis (IUPUI), Indianapolis, Indiana, United States

While isolation is an important property from a security perspective, virtual machines (VMs) often need to communicate and exchange a considerable amount of data. Research in virtualization technology has been focused mainly on increasing isolation of co-resident virtual machines. The isolation properties of virtualization demand that the shared resources are strictly separated. The machine registers are also restricted; therefore virtual machines are forced to fallback to inefficient network emulation for communication. This research is based upon a stealthy way to communicate between virtual machines and virtual machine managers (VMMs) running on the Linux operating system. Virtmon is a paravirtualized virtual machine introspection (PVMI). It is a platform upon which users install and load a group of kernel modules. The Virtmon project utilizes the intra-to-exo channel to communicate stealthily between the virtual machine and its virtual machine manager, and the exo-to-intra channel to communicate stealthily between the virtual machine manager and the virtual machine, using a shadow region. The shadow region hides any activity between the machines and monitor which keeps malware from detecting and hijacking the communication between the two. The unrestricted PVMI framework shifts the challenges from bridging the semantic gap, to protecting and hiding the PVMI mechanism. Therefore, communication is secure, allowing undetected assistance from a privileged VMM to a VM. The Virtmon project has not only allowed the VMM to cross communication barriers undetected, but also allows for unrestricted registers, into which more data can be exchanged.

63 Your data in the cloud: Facts and fears

Sharang Phatak1, sharang.phatak@dotmatics.com, Berkley A Lynch2, Tamsin E Mansley2, Philip Mounteney1, Jess W Sager1. (1) Dotmatics, Inc., San Diego, CA 92121, United States, (2) Dotmatics, Inc., Woburn, MA 01801, United States

Modern research teams are often decentralized, consisting of internal and external partnerships across the globe. Ensuring all the scientists involved have up-to-the-minute access to the project data they need is a challenge that can be met by secure cloud-based software deployments. This allows any scientist with an internet connection and appropriate access control to login to their project web interface to upload new data or review and analyze the current data. We will present solutions and case studies where cloud software deployments are facilitating research and collaboration through secure exchange and sharing data of all types between research partners, collaborators and customers, locally or across the globe. Instant communication through the cloud or local network enables and enriches collaborative research. We will also discuss how cloud-based solutions support the increasing requirements for mobile data access with BYOD (Bring Your Own Device).

74 Cheminfomatics for dye chemistry research: Bringing online an unprecedented 100,000 sample dye library

David Hinks1, dhinks@ncsu.edu, Nelson Vinueza-Benitez1, David C Muddiman2, Antony J Williams3. (1) Department of Textile Engineering, Chemistry &Science, North Carolina State University, Raleigh, North Carolina 27695, United States, (2) Department of Chemistry, North Carolina State University, Raleigh, North Carolina 27695, United States, (3) Department of eScience, Royal Society of Chemistry, Wake Forest, North Carolina 27587, United States

The synthetic organic chemistry industry arguably began with the commercialization of the first synthetic dye, Mauveine, by Sir William Henry Perkin in 1856. Throughout the next 150 years, research and development of dyes exploded in response to the growing demand for high performance colored products for multiple major industries, including textiles, plastics, coatings, cosmetics, and printing. While many thousands of prototype dyes have been designed, synthesized, characterized, and tested, most of the structural and property data have been kept from the open literature even though large segments of the colorant industry have matured and many high volume dyes are now off patent. This is unfortunate considering that dyes are of fundamental importance to a number of growing areas of science and technology, including solar energy capture, medicinal chemistry (e.g. photodynamic therapy for cancer treatment), biomarkers, environmental monitoring, security printing, and camouflage. The ability for all scientists to observe comprehensive dye structure-property relationship data could help advance the theoretical and practical understanding of the role of dyes in various complex systems. NC State University's recently formed Forensic Sciences Institute is building a dye library that will enable establishment of the first comprehensive cheminfomatics system for forensic trace evidence analysis of dyed materials, as well as a broad range of dye discovery projects. As part of this effort, NC State recently secured a remarkable donation of approximately 100,000 dye samples, spectra and performance data that were made by a leading chemical manufacturer over a period of more than 50 years. Significant parts of the library will be made available online for free. The scope and challenges in developing a digitized structural database will be reviewed. Once completed, the new library will provide all scientists with a powerful tool for dye discovery and knowledge.

Tuesday, March 18, 2014

Ethical Considerations in Digital Scientific Communication and Publishing - AM Session

Omni Dallas Hotel
Room: Deep Ellum A
Cosponsored by CHAL, CHED, ETHC, PROF, YCC

Leah McEwen, Barbara Moriarty, Edward Mottel, Heather Tierney, Organizers
Heather Tierney, Presiding
8:00 am - 12:00 pm
8:00 Introductory Remarks
8:05 50 Ethical dilemmas in the creation and sharing of a crystallographic database system

Suzanna Ward, ward@ccdc.cam.ac.uk, Colin R Groom. Cambridge Crystallographic Data Centre, Cambridge, United Kingdom

The Cambridge Crystallographic Data Centre is one of the oldest digital scientific publishers; since 1965 almost 700,000 small molecule crystal structures have been curated and entered into the Cambridge Structural Database. The CCDC continues to process around 200 small molecule crystal structures every day. Advanced software tools are used to determine the 'chemistry' of a molecule represented by the atomic coordinates we receive. In addition, structures are curated by our expert scientific editors. In these processes we find errors, cases of mis-(or over-)interpretation, unintentional redeterminations and the occasional fraudulent structure. All such instances require careful handling and can present ethical dilemmas. To exacerbate difficulties, deposition of experimental data (in the form of structure factors) is not universal in the small molecule crystallographic community. This is unlike the situation with protein structures and one might argue that it is time to mandate experimental data deposition. But who can issue such a mandate and will raising the hurdle for deposition reduce the number of structures deposited and therefore available to others? A further ethical dilemma is presented by the need to fund our efforts. The CCDC receives no direct grant aid for its curation activities. The Centre therefore relies on financial contributions from the users of its systems, often the very same people from whom we have received the data. Although the individual structures we hold are available free at the point of use, in order to ensure financial sustainability, restrictions are placed on the sharing of the contents of the database system. Is it ethically acceptable to have these restrictions?
8:30 51 Image manipulation in scholarly publishing: Setting standards and promoting best practice

Christina Bennett, cbennett@the-aps.org, American Physiological Society, Bethesda, MD 20814, United States

Over the past few years, scholarly publishers, including the American Physiological Society (APS), have experienced a dramatic increase in the number of publication ethics issues. In response, APS has taken several steps to revise the publication process so that articles are reviewed for potential ethical concerns prior to publication. In particular, figures within accepted manuscripts are now screened for image manipulation. Manuscripts with images that appear to contain splicing, extreme contrast adjustment, selective editing, etc. are now placed on hold until the author corrects the figures and/or discloses the modifications. While, the vast majority of the image modifications that are identified are considered to be minor presentation errors, a handful of manuscripts per year contain scientifically inappropriate image manipulation and are not published. Thus, the image review process serves to educate authors on best practice for image preparation and to protect the journal, its authors, and readers, from publishing manuscripts that contain inappropriately prepared data.
8:55 52 Tools for identifying potential misconduct: The CrossCheck service from CrossRef

Rachael Lammey, rlammey@crossref.org, CrossRef, Oxford, United Kingdom

CrossRef is an independent membership association, founded and directed by publishers. The organisation was formed in 2008 and initially focused on digital object identifier (DOI) registration and reference linking using the DOI to create a sustainable infrastructure and interoperability in online scholarly publishing. CrossRef's role in the industry has expanded however, and the organisation now provides a wider range of services that aim to serve the collective needs of the industry. In 2007, the CrossRef board identified plagiarism as an area of concern, and CrossCheck was launched in 2008. CrossCheck uses the iThenticate tool from iParadigms to compare the text of manuscripts to a unique database of content which contains the full-text of articles, books and conference proceedings from over 500 publishers. When a manuscript is uploaded, a report is prepared and presented to an editor so that they can gauge the originality of a piece of text and see where it overlaps with other papers. CrossCheck is now being widely adopted by journals as part of their peer review process, and over 100,000 manuscripts were uploaded to the iThenticate system to be checked in August 2013. This raises a new set of questions however; how to interpret the reports, how to follow-up and what limitations still exist in text-comparison software. Where do we go from here?
9:20 53 Mapping the terrain of publication ethics

Charon A Pierson, cpierson@aanp.org, American Association of Nurse Practioners, Gilbert, AZ 85298, United States

The Committee on Publication Ethics (COPE) has amassed a database of more than 400 cases of ethical misconduct since its inception in 1997. These cases have been presented and discussed at quarterly Fora and were recently analyzed and categorized (Hames, Pierson, Ridgeway, &Barbour, 2013). Case presentation at Fora provided the impetus for the development of many of the COPE resources such as Flowcharts, Guidelines, and Discussion Papers. This presentation will focus on the most common issues arising from the COPE cases: plagiarism, duplicate publication, reviewer misconduct, fabrication or falsification of data, unethical research, and authorship issues. Using case examples, we will explore the resources available from COPE to resolve ethical dilemmas in publishing.
9:45 Intermission
9:55 54 Publication ethics in ACS journals: Education and verification

Anne Coghill, a_coghill@acs.org, Editorial Office Operations, ACS Publications Division, Washington, DC 20036, United States

ACS Publications has a number of programs to educate authors about topics in publication ethics. Additionally, a number of tools are used during manuscript submission and peer review to verify that authors behave in an ethical manner. This presentation will review ACS Publications efforts to ensure the scientific integrity of material published in our journals.
10:20 55 Ethics in scientific publication: Observations of an editor and recommended best practices for authors

Kirk S Schanze, kschanze@chem.ufl.edu, Department of Chemistry, University of Florida, Gainesville, FL 32611, United States

The scientific publishing enterprise is strongly reliant on the ethics of the scientific community. Editors and reviewers do their best to identify areas of concern when a paper is subjected to peer-review, but often those best able to indentify ethical problems are the senior and contributing authors. The most common area of ethical concern is authorship, but prior publication publication and plagiarism also occur with some frequency. The talk will highlight common problems encountered by authors, editors and reviewers related to ethical issues. In addition, best practices will be discussed from the viewpont of the submitting author to alleviate possible ethical problems that may arise upon submission of a paper.
10:45 56 Dealing with scientific misconduct: Part of an editor's day-to-day work

Haymo Ross, hross@wiley.com, Wiley-VCH, Weinheim, Germany

Editors of scholarly journals are very often confronted with different types of scientific misconduct ranging from inadequate citing to outright fraud. In order to deal with this unpleasant aspect of their work they can seek advice from guidelines such as the “Ethical Guidelines for Publication in Journals and Reviews” issued by the EuCheMS. In this lecture, the aforementioned guidelines are used as a common thread to define and explain various categories of scientific misconduct, e.g., plagiarism and self-plagiarism, with a focus on the speaker's own experiences. The responsibility of authors but also reviewers and editors is reviewed and real (though anonymized) cases are given as examples.
11:10 57 Role of the journal editor in maintaining ethical standards in the changing publishing environment

Jamie Humphrey, ruthvens@rsc.org, Sarah Ruthven. Royal Society of Chemistry, Cambridge, United Kingdom

The Royal Society of Chemistry is a leading publisher of chemistry journals. Ethical issues are becoming increasingly easy to detect with new technologies, but are presenting more challenges to resolve. In this talk hear how Editors at the Royal Society of Chemistry are facing the challenge of successfully handling the growing number of ethical issues, with details of the complexities these are presenting to publishers, authors, reviewers and editors. Ethical issues covered in this presentation will include authorship disputes, plagiarism of content and fabrication of results, with the Editors explaining how they approach these situations.
11:35 Panel Discussion moderated by Gregory Ferrence

Tuesday, March 18, 2014

Cloud Computing in Cheminformatics - PM Session

Omni Dallas Hotel
Room: Deep Ellum A
Cosponsored by COMP

Rudolph Potenzone, Organizers
Rudolph Potenzone, Presiding
1:40 pm - 5:30 pm
1:40 Introductory Remarks
1:45 58 10 Years of collaborative drug discovery in the cloud

Barry A. Bunin, bbunin@collaborativedrug.com, Science, Collaborative Drug Discovery, Burlingame, CA 94010, United States

The CDD Vault is a Cloud (Secure, Hosted) full featured solution for drug discovery, including chemical registration, dose response, SAR tools, and collaborative sharing. By layering unique collaborative capabilities upon requisite drug discovery database functionality unlocks and amplifies latent synergy between biologists and chemists. The application of collaborative technologies to interrogate potency, selectively, and therapeutic windows of small molecule enzyme, cell, and animal study data will be presented. An example combining integrated bioinformatics and chemoinformatics with in vitro experimental validation to identify two leads against putative new Tuberculosis targets (in collaboration with SRI's Computer Science + Bioscience Divisions), a second example to overcome malaria chloroquine resistance (USA - South Africa four team collaboration), a third example with the TB Drug Accelerator Consortium (involving multiple collaborators plus selective disclosure between seven big pharmas with the BMGF), and a fourth example broadly across CNS therapeutic areas (in collaboration with the NIH Neuroscience Blueprint) demonstrate the general concept that a more effective collaborative model is possible today using secure, web-based collaborative technologies to bring together complementary, specialized expertise. Finally, a commercial use case working with Acetylon Pharmaceuticals from academic spinout (of Harvard) of the initial IP to working with CROs (in China) to bringing small molecules against Epigenetic targets (HDACs) into clinical trials will be shared. Securely integrating private with external data is a key capability which allows collaborative technologies like the CDD Vault to scalably handle IP-sensitive data.
2:15 59 Cloud-hosted APIs for cheminformatics designed for real time user interfaces

Alex M Clark, aclark@molmatinf.com, R&D, Molecular Materials Informatics, Montreal, QC H3J2S1, Canada

The modern trend toward cloud computing coincides with a new generation of user interface paradigms that are based on web apps or native mobile apps. Both of these platforms have enormous advantages in terms of deployment methods and the ability to provide an omnipresent user experience, but unlike traditional applications from the desktop era, they are not appropriate for intensive calculations or storage of large quantities of data. In order to make them as useful as possible, it is often necessary to outsource computation and storage, which is typically done by using a web API. The process of decoupling user interface and computation/storage is often not a simple matter, and considerable foresight and careful design is necessary when designing cheminformatics functionality that can be integrated into a seemless and responsive user experience. Particular examples will be given using mobile apps, and attention given to the partitioning between the computational features that are best localized on the device, and those that are best performed on a powerful server. Considerations include deciding how much functionality to offload, balancing latency vs. responsiveness, and the issues involved in creating an asynchronous task and the relatively high inconvenience of providing progress indicators and the ability to cancel a task. The strategies used by apps such as the Mobile Molecular DataSheet (MMDS), SAR Table and MolPrime+ will be discussed in detail.
2:45 pm 60 WITHDRAWN
3:15 Intermission
3:30 61 Application of cloud computing to Royal Society of Chemistry data platforms

Valery Tkachenko, tkachenkov@rsc.org, Ken Karapetyan, Jon Steele, Alexey Pshenichnov, Antony J. Williams. eScience, Royal Society of Chemistry, Cambridge, Cambridgeshire CB4 0WF, United Kingdom

Cloud computing offers significant advantages for the hosting of RSC chemistry databases in terms of reliability, performance and access to large scale computational power. The ChemSpider database contains almost 30 million unique chemical compounds and access to compute power to regenerate properties and add new properties is essential for efficient delivery on a manageable timescale. The use of cloud-based facilities reduces the needs for internal infrastructure and enhances performance generally at the cost of significant recoding of the platforms. This presentation will review our move of our ChemSpider related projects to the cloud, the associated challenges and both the obvious and unforeseen benefits. We will also discuss our use of parallelization technologies for mass calculation using Hadoop.
4:00 62 PubChem in the cloud

Paul Thiessen, Bo Yu, Gang Fu, Evan Bolton, bolton@ncbi.nlm.nih.gov. National Center for Biotechnology Information, Bethesda, MD 20894, United States

What is 'cloud computing'? Depending on who you ask, you get the notion that information is stored, managed, and processed somewhere 'out there' in the wild yonder of the Internet. PubChem is an on-line archive of chemical substance information and their biological activities. Depending on your perspective, PubChem can be used as a 'cloud' in that you can access, search, and analyze scientific information available in PubChem using various programmatic interfaces. PubChem information can also be put into a 'cloud' and made available. This talk will demonstrate ways one can use PubChem as a 'cloud' or from a 'cloud'.
4:30 63 Your data in the cloud: Facts and fears

Sharang Phatak1, sharang.phatak@dotmatics.com, Berkley A Lynch2, Tamsin E Mansley2, Philip Mounteney1, Jess W Sager1. (1) Dotmatics, Inc., San Diego, CA 92121, United States, (2) Dotmatics, Inc., Woburn, MA 01801, United States

Modern research teams are often decentralized, consisting of internal and external partnerships across the globe. Ensuring all the scientists involved have up-to-the-minute access to the project data they need is a challenge that can be met by secure cloud-based software deployments. This allows any scientist with an internet connection and appropriate access control to login to their project web interface to upload new data or review and analyze the current data. We will present solutions and case studies where cloud software deployments are facilitating research and collaboration through secure exchange and sharing data of all types between research partners, collaborators and customers, locally or across the globe. Instant communication through the cloud or local network enables and enriches collaborative research. We will also discuss how cloud-based solutions support the increasing requirements for mobile data access with BYOD (Bring Your Own Device).
5:00 64 Moving main stream chemical research to the cloud

Philip J. Skinner, Philip.skinner@perkinelmer.com, Joshua Bishop, Phil McHale, Rudy Potenzone. PerkinElmer, United States

Despite the advent of cloud computing, and the prevalence of applications such as GoogleDocs and Gmail, few laboratory specific applications have appeared. We will present a new platform that promises to rethink the ways scientists collect, store, share and learn from scientific observations by fully embracing the cloud philosophy. Reimagining ChemDraw for a new platform led to new ways of driving scientific collaboration. In a similar vein we have assembled a novel environment that allows scientists to gather information about their experiments, document the results, share knowledge and discuss the implications of their knowledge. Through annotations and comments within a project, scientists can collaborate in real time to try out new ideas while they share suggestions and explore new directions. By leveraging the power of crowd-sourcing we are able to rapidly adapt to changing needs and environment and optimize the full user experience from novice through user to advocate.

Wednesday, March 19, 2014

New Models in Substance Discovery - AM Session

Omni Dallas Hotel
Room: Deep Ellum A

Roger Schenck, Organizers
Roger Schenck, Presiding
8:10 am - 12:00 pm
8:10 Introductory Remarks
8:15 65 Functional requirements for chemical information retrieval for intellectual property professionals

Matthew McBride, mmcbride@cas.org, Science IP, Chemical Abstracts Service, Columbus, Ohio 43202, United States

Chemical information retrieval by intellectual property (IP) professionals requires similar functionality to end user scientists – quality content and advanced search functionality. However, IP professionals are additionally concerned with comprehensive retrieval from worldwide sources (patent authorities and non-patent literature), exemplified substance collections and Markush disclosures, association with the original citations or sources, and post-processing results from multiple search platforms. Therefore the required features of their search tools are often more demanding, requiring additional functionality to manage workflow in navigating and presenting results to a wide-array of technical users, from scientists to patent attorneys. This session focuses on providing insight from search professionals on key functional requirements for chemical information systems used in IP work, along with search examples demonstrating these features from databases on STN, Questel MMS and other search platforms.
8:45 66 New approaches to search interfaces in PubChem

Asta Gindulyte, Lianyi Han, Paul Thiessen, Bo Yu, Lewis Geer, Evan Bolton, bolton@ncbi.nlm.nih.gov. National Center for Biotechnology Information, Bethesda, MD 20894, United States

Providing easy to use web-based scientific search interfaces is a challenge. This is true for several reasons. Firstly, the devices accessing scientific information are diverse with potentially big differences in screen display size, network speed, network latency, and interface (e.g., touch-based vs. mouse-based). Secondly, the amount of publically available scientific data is growing markedly. For example, the open and free PubChem resource (http://pubchem.ncbi.nlm.nih.gov) currently contains more than 47 million unique small molecules derived from 120 million substance sample descriptions and 217 million bioactivity results from 717 thousand biological experiments. Thirdly, the availability and diversity of scientific information is very uneven between substances, with some chemicals being well studied and others being almost completely unknown. This presentation will explore ways in which PubChem is adapting, including: making search interfaces adapt to the device accessing it, developing new algorithms that determine result relevancy, and harnessing new technologies to improve the speed and scalability of substance searching.
9:15 67 From searching to finding: New developments for managing large data sets

Juergen Swienty-Busch1, j.swienty-busch@elsevier.com, David Evans2. (1) Elsevier Information Systems GmbH, Frankfurt, Hessen 60486, Germany, (2) Reed Elsevier Properties SA, Neuchatel, Switzerland

A challenge for a system that is designed to support chemistry researchers across all industries and academic environments is usability and relevancy. A chemical engineer in a chemical company has different expectations for a system serving his information needs when compared to a medicinal chemist in a pharma company or a PhD student in an inorganic lab at a university. We will describe recent developments in the Reaxys product family that address these challenges with a new and highly customizable user interface combined with an extended data set and will present use cases and applications that demonstrate its applicability in various chemistry workflows.
9:45 68 Search and navigation functionality for a major reference work online: SOS 4.0

Fiona Shortt de Hernandez1, fiona.shortt@thieme.de, Guido F. Herrmann1, Peter Loew2. (1) Thieme Publishers, Stuttgart, Germany, (2) InfoChem GmbH, Munich, Germany

There are significant challenges associated with making content from a multiauthor reference work searchable, retrievable and readable online. This task was made more complicated in the case of Science of Synthesis because of the scale and scope of the project. The online product which includes the Houben–Weyl archive (going back 100 years) covers hundreds of volumes and thousands of pages with contributions from over 1,500 authors. Science of Synthesis is now a unique, structure searchable, full-text resource in organic synthesis that provides the user with expert-evaluated methods. The online product combines full-text browsing functionality together with InfoChem's modern structure and reaction search capabilities. This talk describes how we overcame the various technical hurdles in order to achieve this. We also give specific examples of the features and functionality included in the product in order to help the researcher gain access to relevant content quickly. For example: A clean and simple user-interface design makes comprehensive searching straightforward. Useful navigation aids such as breadcrumbs and an interactive table of contents facilitate browsing. Intuitive text search options allow quick access to relevant content. Advanced text searching options help the user to define more complicated queries. The manual preparation of a name reaction index and the use of deep indexing enable the association of transformations with specific named reactions even if they are not mentioned as such in the full text. The “All-in-One” structure and reaction search from InfoChem provides a broader spectrum of weighted hits. The relevant ranking of hits using the InfoChem algorithm for structure and reaction searching as well as the MarkLogic algorithm for text searching helps the user to rate the quality of their results quickly and determine which information is of interest to them. Faceted navigation of the hitlist helps the user to further refine their results.
10:15 Intermission
10:30 69 Chemical most common denominator: Use of chemical structures for semantic enrichment and interlinking of scientific information

Valentina Eigner-Pitto, ve@infochem.de, Josef Eiblmaier, Hans Kraut, Larisa Isenko, Heinz Saller, Peter Loew. InfoChem GmbH, Munich, Germany

Academic and industrial researchers nowadays expect interactive, easy to use access to the scientific literature and supplementary information in order to satisfy their information needs quickly and comprehensively. To address these challenges major scientific publishers have begun to chemically enhance/enrich their scientific articles, reference works and eBooks with information based on chemical structures and reactions. Compound indexing, highlighting of chemical terms, one-click display of additional compound attributes and, most important, semantic linking to other relevant resources or information have been implemented. First and foremost enabling chemical structure searching in text sources offers benefits to the user never seen before by providing an additional, precise entry point to the full text. Sophisticated cutting edge technologies like chemical named entity extraction, chemical image recognition and automatic work-up of ChemDraw files are applied to fulfill these requirements. This lecture will give an overview of current implementations of the concepts listed above and will illustrate the benefits as well as the challenges and pitfalls by one concrete example project.
11:00 70 Representation and display of non-standard peptides using semi-systematic amino acid monomer naming

Roger A Sayle, roger@nextmovesoftware.com, Noel M O'Boyle. NextMove Software, Cambridge, CAMBS CB4 0EY, United Kingdom

The registration of peptide and peptide-like structures in chemical databases poses a number of technical challenges, as do other biological oligomers. Primary among these are the size and complexity of these compounds, often making it difficult or impossible for a biochemist to identify differences or similarities between compounds stored as all-atom representations. For biological (proteinogenic) sequences the solution is simple, to use strings of the one (or three) letter codes to represent the biopolymer. However, for post-translationally modified, D-, cyclic and non-standard peptides the way forward is less clear. One approach is to use an ever larger dictionary three letter codes to encode common non-standard amino acids. Unfortunately, this method quickly becomes unwieldy once the set of abbreviations exceeds those frequently encountered in the literature, requiring a chemist to consult a key or dictionary for entry or interpretation of structures. In this presentation, we propose the use of semi-systematic monomer names, based upon readily recognizable chemical line formulae, for the encoding and display of traditionally difficult to handle peptides. These rules lead to names such as N(Me)Ser(tBuOH) that are similar to those seen/used in scientific publications, though not formally ratified by IUPAC nor CAS.

11:30 71 New structure search capabilities for accessing CAS content

Kurt Zielenbach1, kzielenbach@cas.org, Bryan Harkleroad2. (1) Marketing, CAS, Columbus, Ohio 43202, United States, (2) Product Development, CAS, Columbus, Ohio 43202, United States

Access to comprehensive, high quality chemical information by research scientists is essential for ensuring successful research projects. As the number of known substances, reactions and related literature continues to grow exponentially, chemists require fast, intuitive and relevant access to this information through various access paths - particularly by chemical structure techniques. This session focuses on new technologies in development at CAS that will help chemists improve efficiencies in searching and decision making with SciFinder® – the choice for chemistry research.™ Chemical Abstracts Service (CAS), a division of the American Chemical Society, is the world's authority for chemical information and the only organization in the world whose objective is to find, collect and organize all publicly disclosed chemical substance information.

Wednesday, March 19, 2014

General Papers - PM Session

Omni Dallas Hotel
Room: Deep Ellum A

Jeremy Garritano, Erin Bolstad, Organizers
Erin Bolstad, Presiding
1:30 pm - 3:30 pm
1:30 72 UK National Chemical Database Service: An integration of commercial and public chemistry services to support chemists in the United Kingdom

Antony J. Williams, williamsa@rsc.org, Valery Tkachenko, Richard Kidd. eScience, Royal Society of Chemistry, Cambridge, Cambridgeshire CB4 0WF, United Kingdom

At a time when the data explosion has simply been redefined as “Big”, the hurdles associated with building a subject-specific data repository for chemistry are daunting. Combining a multitude of non-standard data formats for chemicals, related properties, reactions, spectra etc., together with the confusion of licensing and embargoing, and providing for data exchange and integration with services and platforms external to the repository, the challenge is significant. This all at a time when semantic technologies are touted as the fundamental technology to enhance integration and discoverability. Funding agencies are demanding change, especially a change towards access to open data to parallel their expectations around Open Access publishing. The Royal Society of Chemistry has been funded by the Engineering and Physical Science Research of the UK to deliver a “chemical database service” for UK scientists. This presentation will provide an overview of the challenges associated with this project and our progress in delivering a chemistry repository capable of handling the complex data types associated with chemistry. The benefits of such a repository in terms of providing data to develop prediction models to further enable scientific discovery will be discussed and the potential impact on the future of scientific publishing will also be examined.
2:00 73 Data enhancing the Royal Society of Chemistry publication archive

Antony J. Williams, williamsa@rsc.org, Colin Batchelor, Peter Corbett, Ken Karapetyan, Valery Tkachenko. eScience, Royal Society of Chemistry, Cambridge, Cambridgeshire CB4 0WF, United Kingdom

The Royal Society of Chemistry has an archive of hundreds of thousands of published articles containing various types of chemistry related data – compounds, reactions, property data, spectral data etc. RSC has a vision of extracting as much of these data as possible and providing access via ChemSpider and its related projects. To this end we have applied a combination of text-mining extraction, image conversion and chemical validation and standardization approaches. The outcome of this project will result in new chemistry related data being added to our chemical and reaction databases and in the ability to more tightly couple web-based versions of the articles with these extracted data. The ability to search across the archive will be enhanced as a result. This presentation will report on our progress in this data extraction project and discuss how we will ultimately use similar approaches in our publishing pipeline to enhance article markup for new publications.
2:30 74 Cheminfomatics for dye chemistry research: Bringing online an unprecedented 100,000 sample dye library

David Hinks1, dhinks@ncsu.edu, Nelson Vinueza-Benitez1, David C Muddiman2, Antony J Williams3. (1) Department of Textile Engineering, Chemistry &Science, North Carolina State University, Raleigh, North Carolina 27695, United States, (2) Department of Chemistry, North Carolina State University, Raleigh, North Carolina 27695, United States, (3) Department of eScience, Royal Society of Chemistry, Wake Forest, North Carolina 27587, United States

The synthetic organic chemistry industry arguably began with the commercialization of the first synthetic dye, Mauveine, by Sir William Henry Perkin in 1856. Throughout the next 150 years, research and development of dyes exploded in response to the growing demand for high performance colored products for multiple major industries, including textiles, plastics, coatings, cosmetics, and printing. While many thousands of prototype dyes have been designed, synthesized, characterized, and tested, most of the structural and property data have been kept from the open literature even though large segments of the colorant industry have matured and many high volume dyes are now off patent. This is unfortunate considering that dyes are of fundamental importance to a number of growing areas of science and technology, including solar energy capture, medicinal chemistry (e.g. photodynamic therapy for cancer treatment), biomarkers, environmental monitoring, security printing, and camouflage. The ability for all scientists to observe comprehensive dye structure-property relationship data could help advance the theoretical and practical understanding of the role of dyes in various complex systems. NC State University's recently formed Forensic Sciences Institute is building a dye library that will enable establishment of the first comprehensive cheminfomatics system for forensic trace evidence analysis of dyed materials, as well as a broad range of dye discovery projects. As part of this effort, NC State recently secured a remarkable donation of approximately 100,000 dye samples, spectra and performance data that were made by a leading chemical manufacturer over a period of more than 50 years. Significant parts of the library will be made available online for free. The scope and challenges in developing a digitized structural database will be reviewed. Once completed, the new library will provide all scientists with a powerful tool for dye discovery and knowledge.
3:00 75 QM/MM docking for GPCR targets

Art E Cho, artcho@korea.ac.kr, Minsup Kim. Department of Bioinformatics, Korea University, Seoul, Republic of Korea

The study of GPCR's as drug targets have been intensified in recent days as more and more X-ray structures of GPCR are solved. In fact, awarding of the 2012 Nobel prize in chemistry to Lefkowitz and Kobilka was just the beginning of the race to the discovery of GPCR targeted drugs. Many research groups have been trying to use current-state docking programs for screening of compound libraries against GPCR targets to varying degrees of success. As many people in the computational drug discovery community know by now, there is even a CASP-style competition dedicated to GPCR targeted docking. Docking to GPCR targets is in many ways quite different from docking to other targets. Binding sites of GPCR's are generally open and flexible. One must consider these peculiarities for GPCR docking. Over the years we have developed docking methodologies utilizing QM/MM calculations in order to take into account of phenomena that cannot be described by conventional force fields. Recently we devised a docking protocol based on these QM/MM docking methods, combined with induced fit docking and solvent calculations with GPCR targets in mind. Application of this protocol to a set of known GPCR cocrystal structures reveals that when the particularities of GPCR binding sites are carefully treated, the performance of docking to GPCR can be greatly enhanced.

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Future ACS National Meetings

Meeting Date Year City Theme

247th

Mar. 16–20

2014

Dallas, TX

Chemistry and Materials for Energy

248th

Aug. 10–14

2014

San Francisco, CA

Chemistry and Global Stewardship

249th

Mar. 22–26

2015

Denver, CO

Chemistry of Natural Resources

250th

Aug. 16–20

2015

Boston, MA

Innovation from Discovery to Application

251st

Mar. 13–17

2016

San Diego, CA

TBD

252nd

Aug. 21–25

2016

Philadelphia, PA

TBD

253rd

Apr. 2–6

2017

San Francisco, CA

 TBD

254th

Aug. 20–24

2017

Washington, DC

TBD

255th

Mar. 18–22

2018

New Orleans, LA

TBD

256th

Aug. 19–23

2018

Boston, MA

TBD

257th

Mar. 31–Apr. 4

2019

Orlando, FL

TBD

258th

Aug. 25–29

2019

San Diego, CA

TBD

 

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