Technical Program Listing

ACS Chemical Information Division (CINF)
246th ACS National Meeting, Fall 2013
Indianapolis, IN (September 8-12)

CINF Symposia

J. Garritano, Program Chair

Sunday, September 8, 2013

Current Challenges in Cheminformatics: Exploiting Information and Knowledge in Structured and Unstructured Environments - AM Session Cheminformatics Tools and Methods
Indiana Convention Center
Room: 140
Cosponsored by COMP
Neil Kirby, Dirk Tomandl, Organizers
Dirk Tomandl, Presiding
8:10 am - 12:00 pm
8:10   Introductory Remarks
8:15 1 New insights and tools for capturing, validating, and utilizing structure/property data: Curiously similar approaches for drug discovery and materials science

Curt M Breneman, brenec@rpi.edu, Ke Wu, Lisa Morkowchuk, Jed Zaretzki, Sourav Das, Michael Krein.
Abstract

8:45 2 Scaffold-based reasoning approaches for cross-assay structure-activity relationship identification

Christos A Nicolaou, c.nicolaou@lilly.com, Quan Liao, Suntara Cahya, Jibo Wang.
Abstract

9:15 3 Knowledge mining by structure search

Jinbo Lee, jlee@scilligence.com,
Abstract

9:45   Intermission
9:55 4 Computational approach of thermodynamic fragmentation applied to formulating badly soluble actives

Johannes Fraaije1,2, j.fraaije@chem.leidenuniv.nl, Monica Bulacu2, Ruben Gracia2, Shyamal K Nath2.
Abstract

10:25 5 Spaghetti seas and filter forests: Navigating Pipeline Pilot protocol creation with maintenance in mind

Jennifer L Heymont, Jennifer_Heymont@eisai.com,
Abstract

10:55 6 New frontier in reaction search: Dynamic mining of ELN based reaction methodology data in Spotfire®

Philip J Skinner, Philip.skinner@perkinelmer.com, Rudy Potenzone, Megean Schoenberg, Amy Kallmerten, Phil McHale, Michael Swartz.
Abstract

11:25 7 Plexus: A clean web application for structural data analysis

David Deng, ddeng@chemaxon.com, Andras Stracz.
Abstract

11:55   Concluding Remarks

Sunday, September 8, 2013

Chemistry on Tablet Computers - AM Session
Indiana Convention Center
Room: 141
David Martinsen, Martin Braendle, Organizers
Martin Braendle, Presiding
8:05 am - 12:00 pm
8:05   Introductory Remarks
8:10 8 Apps and approaches to mobilizing chemistry from the Royal Society of Chemistry

Antony J. Williams1, williamsa@rsc.org, Valery Tkachenko1, Dmitry Ivanov1, Will Russell2.
Abstract

8:40 9 ChemDraw, iPads, and collaboration tools in the classroom: Results of a joint PerkinElmer and McGraw Hill pilot at the organic chemistry undergraduate level

Robin Y Smith1, robin.smith@perkinelmer.com, Hans C Keil1, hans.keil@perkinelmer.com, Tamara Hodge2.
Abstract

9:10 10 Can I get that to go? Reading research articles on a tablet

Jeff Lang, j_lang@acs.org,
Abstract

9:40   Intermission
9:55 11 JSmol: Full-service molecular visualization on the Web without Java

Robert Hanson1, hansonr@stolaf.edu, Zhou Renjian4, Takanori Nakane2, Paul Pillot3.
Abstract

10:25 12 Enabling chemistry on-the-go with modern solutions

Tamsin E Mansley1, tamsin.mansley@dotmatics.com, Graeme E Dennis1, Shikha O'Brien2.
Abstract

10:55 13 Tablets in the lab: Enabling the flow of chemical synthesis data into a chemistry repository

Simon J Coles1, s.j.coles@soton.ac.uk, Richard J Whitby1, Aileen Day2, Cerys Willoughby1, Valery Tkachenko2, Jeremy G Frey1, Antony J Williams2.
Abstract

11:25 14 New strategy to engage mobile computing users and developers

Steven M Muskal, smuskal@eidogen-sertanty.com,
Abstract

11:55   Concluding Remarks

Sunday, September 8, 2013

Current Challenges in Cheminformatics: Exploiting Information and Knowledge in Structured and Unstructured Environments - PM Session Data Access, Usage and Pitfalls
Indiana Convention Center
Room: 140
Cosponsored by COMP
Dirk Tomandl, Neil Kirby, Organizers
Dirk Tomandl, Presiding
1:10 pm - 3:50 pm
1:10   Introductory Remarks
1:15 15 Improving access to data: A distributed approach

Graeme E Dennis1, graeme.dennis@dotmatics.com, Tamsin E Mansley1, Shikha O'Brien2.
Abstract

1:45 16 Digital fractionation: Using NoSQL technology to extract biochemical data from big data repositories

Lewis Y Geer, lewis.geer@nih.gov, Lianyi Han, Yanli Wang, Evan E Bolton, Siqian He, Bo Yu.
Abstract

2:15   Intermission
2:20 17 Exploring interconnectivity of molecular biology databases and data mining tools

Stefan M Furrer, stfurrer@indiana.edu, David J Wild.
Abstract

2:50 18 Caveats in the use of pharmaceutical drug discovery data

Terry R Stouch, tstouch@gmail.com,
Abstract

3:20 19 Extracting synthetic knowledge from reaction databases

Orr Ravitz1, ravitz@simbiosys.com, James Law1, Anthony Cook2, A. Peter Johnson2.
Abstract

Sunday, September 8, 2013

Current Challenges in Cheminformatics: Exploiting Information and Knowledge in Structured and Unstructured Environments - PM Session Chemical Structures in Documents
Indiana Convention Center
Room: 140
Cosponsored by COMP
Dirk Tomandl, Neil Kirby, Organizers
Dirk Tomandl, Presiding
4:00 pm - 5:30 pm
4:00 20 Validation and characterization of chemical structures derived from names and images in scientific documents

John B Kinney, john.b.kinney@dupont.com,
Abstract

4:30 21 Tackling the difficult areas of chemical entity extraction: Misspelt chemical names and unconventional entities

Daniel M Lowe, daniel@nextmovesoftware.com, Roger A Sayle.
Abstract

5:00 22 OPSIN: Taming the jungle of IUPAC chemical nomenclature

Daniel M Lowe, daniel@nextmovesoftware.com, Peter Murray-Rust, Robert C Glen.
Abstract

Sunday, September 8, 2013

Graduate Student Research Symposium in Cheminformatics, Information Science, and Library Science - PM Session
Indiana Convention Center
Room: 141
Cosponsored by COMP
Gary Wiggins, Organizers
Gary Wiggins, Presiding
2:00 pm - 5:25 pm
2:00   Introductory Remarks
2:05 23 Open chemical information: Comparison of Chemical Information Sources (CIS) Wikibook and eXplore Chemical Information Teaching Resources (XCITR)

Yan He, yh4@iuk.edu,
Abstract

2:35 24 Retractions in chemistry: Prevalence and impact

Elsa Alvaro, ealvaro@indiana.edu,
Abstract

3:05 25 Informatics tools for interacting with literature and chemical databases to build pharmacological networks of drug-induced neuropathy

Junguk Hur1,3, juhur@umich.edu, Abra Guo2, Eva L. Feldman1, Jane P.F. Bai3.
Abstract

3:35   Intermission
3:50 26 Molecular scaffolds are special and useful guides to discovery

Jeremy J Yang1,2, jjyang@salud.unm.edu, Cristian G Bologa1, David J Wild2, Tudor I Oprea1.
Abstract

4:20 27 Identification and quantification of glycans in glycomics: Towards biomarker discovery for human diseases

Chuan-Yih Yu, chuyu@indiana.edu, Anoop Mayampurath, Haixu Tang.
Abstract

4:50 28 Probabilistic inference of reactions and ligands in human gut microbial communities from metagenomic sequences

Dazhi Jiao, djiao@indiana.edu, David J Wild.
Abstract

5:20   Concluding Remarks

Sunday, September 8, 2013

CINF Scholarship for Scientific Excellence - EVE Session
Indiana Convention Center
Room: Wabash Blrm 1/2
Guenter Grethe, Organizers
, Presiding
6:30 pm - 8:30 pm
  29 Enhanced ranking of PknB inhibitors using data fusion methods

Abhik Seal, abseal@indiana.edu, David John Wild.
Abstract

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

Ahmed El Kerdawy1, ahmed.elkerdawy@chemie.uni-erlangen.de, Stefan Güssregen2, Hans Matter2, Matthias Hennemann1,3, Timothy Clark1,3,4.
Abstract

31 Harvard Clean Energy Project: From big data and cheminformatics to the rational design of molecular OPV materials

Johannes Hachmann, jh@chemistry.harvard.edu, Roberto Olivares-Amaya, Alan Aspuru-Guzik.
Abstract

Monday, September 9, 2013

Integrative Chemogenomics Knowledge Mining Using NIH Open Access Resources - AM Session
Indiana Convention Center
Room: 140
Rajarshi Guha, Tudor Oprea, Paul Clemons, Organizers
Rajarshi Guha, Presiding
8:50 am - 12:00 pm
8:50   Introductory Remarks
8:55 32 Pushing chemical biology data through the pipes: Architecting and extending the BARD API

Rajarshi Guha, rajarshi.guha@gmail.com, John Braisted, Ajit Jadhav, Dac-Trung Nyguen, Tyler Peryea, Noel Southall.
Abstract

9:20 33 QSAR modeling on the web

Diane Pozefsky2, pozefsky@cs.unc.edu, Diptorup Deb2, Chi Xie2, Alexander Sedykh1, Alex Tropsha1.
Abstract

9:45 34 Data curation and formal BioAssay Ontology (BAO)-based annotations of the DrugMatrix enable bioactivity-based target-relationship analysis and demonstrate incorporation of external datasets into the BioAssay Research Database (BARD)

Tudor Oprea1, toprea@salud.unm.edu, Stephan Schurer2,3, Ahsan Mir3, Uma Vempati3, Jeremy Yang1, Oleg Ursu1, Christian Bologa1.
Abstract

10:10   Intermission
10:20 35 Development of the BioAssay Research Database (BARD): A user-friendly perspective based on active participation from biologists and chemists

Eric S Dawson1,4,6, eric.dawson@vanderbilt.edu, Shaun R Stauffer2,3,5,6, Craig W Lindsley2,3,5,6.
Abstract

10:45 36 BADAPPLE promiscuity plugin for BARD: Evidence-based promiscuity scores

Jeremy J Yang1, jeremyjyang@gmail.com, Oleg Ursu1, Cristian G Bologa1, Anna Waller2, Larry A Sklar2, Tudor I Oprea1.
Abstract

11:30   Panel Discussion

Monday, September 9, 2013

Role and Value of Social Networking in Advancing the Chemical Sciences - AM Session Social Media for the Individual Scientist and to Support Education
Indiana Convention Center
Room: 141
Cosponsored by CHED, SCHB, YCC
Antony Williams, Jennifer Maclachlan, Organizers
Jennifer Maclachlan, Presiding
8:15 am - 12:00 pm
8:15   Introductory Remarks
8:20 37 @ChemConnector and my personal experiences in participating in the expanding social networks for science

Antony J. Williams, williamsa@rsc.org,
Abstract

8:45 38 Get to the point! Techniques for organizing your online social networking skills

Tom Ruginis, happilabs@gmail.com,
Abstract

9:10 39 Plum Analytics: An altmetrics tool for determining impact in the chemical sciences

Andrea M Michalek, andrea@plumanalytics.com,
Abstract

9:35   Intermission
9:45 40 Using social tools collaboratively to communicate and advance science

Christopher McCarthy, c_mccarthy@acs.org, Christine Brennan-Schmidt, c_schmidt@acs.org.
Abstract

10:10 41 Social media in cheminformatics education

David J Wild1, djwild@indiana.edu, Robert Belford2.
Abstract

10:35 42 ChemConf to ConfChem: Twenty years and counting

Robert E. Belford1, rebelford@ualr.edu, Harry E. Pence2.
Abstract

11:00   Intermission
11:10 43 Small chemical businesses and the importance of being social

Jennifer L Maclachlan, pidgirl@gmail.com,
Abstract

11:35 44 XCITR (Explore Chemical Information Teaching Resources): A community resource for chemistry instructors, chemistry librarians, and chemical information providers

Grace Baysinger1, graceb@stanford.edu, Andrea Twiss-Brooks2, Guenter Grethe3, Gregor Fels4.
Abstract

Monday, September 9, 2013

Science-Based Policy Development in the Environment, Food, Health, and Transport Sectors - PM Session
Indiana Convention Center
Room: 140
Cosponsored by AGFD, ANYL, ENVR, MEDI
William Town, Organizers
William Town, Presiding
1:15 pm - 5:05 pm
1:15   Introductory Remarks
1:20 45 Adaptive management tools for engineered nanomaterials in municipal wastewater effluents

Thomas A. Duster, tduster@nd.edu,
Abstract

1:50 46 Role of STEM data and information in an environmental decision-making scenario: The case of climate change

Frederick W Stoss, fstoss@buffalo.edu,
Abstract

2:20 47 Identification of pathways of toxicity to predict human effects

Helena T Hogberg, hhogberg@jhsph.edu, Thomas Hartung.
Abstract

2:50   Intermission
3:05 48 Role of education and training in supporting science-based policy development

Rodger D Curren, rcurren@iivs.org, Hans A Raabe, Brian C Jones.
Abstract

3:35 49 Policy divergence in the absence of science: The case of e-cigarettes

Julie Jones, julie.jones@cncbio.com, David Lawson.
Abstract

4:05 50 Role of regulatory science in reducing the public health impact of tobacco use

Christopher J Proctor, christopher_proctor@bat.com, Chuan Liu.
Abstract

4:35 51 Systematic and structural risk analysis approaches for establishing maximum levels of essential nutrients and other bioactive substances in fortified foods and food supplements

David P Richardson, info@dprnutrition.com,
Abstract

Monday, September 9, 2013

Role and Value of Social Networking in Advancing the Chemical Sciences - PM Session Social Media to Share Science with the Community and the Sharing of Chemical Information
Indiana Convention Center
Room: 141
Cosponsored by CHED, SCHB, YCC
Antony Williams, Jennifer Maclachlan, Organizers
Antony Williams, Presiding
1:00 pm - 3:45 pm
1:00 52 Exploiting the digital landscape to advance the chemical sciences

Bibiana Campos-Seijo, camposseijob@rsc.org, Will Russell, Vibhuti Patel.
Abstract

1:25 53 Using social media as a way to communicate science to the community

George Ruger, gruger04@yahoo.com,
Abstract

1:50 54 Collaborating to convey chemical knowledge through Wikipedia

Martin A Walker, walkerma@potsdam.edu,
Abstract

2:15   Intermission
2:25 55 Tools and strategies for sharing chemical information and research on the web

Jean-Claude Bradley1, bradlejc@drexel.edu, Andrew Lang2.
Abstract

2:50 56 Social networking and PubChem

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

3:15   Panel Discussion
3:40   Concluding Remarks

Monday, September 9, 2013

Joint CINF-CSA Trust Symposium: Semantic Technologies in Translational Medicine and Drug Discovery - PM Session
Indiana Convention Center
Room: 142
David Wild, Jan Kuras, Organizers
David Wild, Jan Kuras, Presiding
1:30 pm - 5:25 pm
1:30   Introductory Remarks
1:35 57 Building support for the semantic web for chemistry at the Royal Society of Chemistry

Valery Tkachenko1, tkachenkov@rsc.org, Colin Batchelor2, Jon Steele2, Alexey Pshenichnov1, Antony J. Williams1.
Abstract

2:05 58 PubChemRDF: Towards a semantic description of PubChem

Evan Bolton, bolton@ncbi.nlm.nih.gov, Gang Fu, Paul Thiessen, Asta Gindulyte.
Abstract

2:35 59 Semantic annotation of PubChem databases

Gang Fu1, gang.fu@nih.gov, Colin Batchelor2, Michel Dumontier3, Janna Hastings4,5, Hande Küçük6, Stephan Schurer6,7, Uma Vempati6, Egon Willighagen8, Evan Bolton1.
Abstract

3:05   Intermission
3:20 60 Practical semantics in the pharmaceutical industry: The Open PHACTS project

Antony J. Williams, williamsa@rsc.org,
Abstract

3:50 61 Enabling the translational medicine and drug discovery information workflow

David Evans1, david.evans@reedelsevier.ch, Timothy Hoctor2, Jacqui Mason2, Pieder Caduff1.
Abstract

4:20 62 Standardized drug and pharmacological class network in ontology representation

Qian Zhu, zhu.qian@mayo.edu, Cui Tao, Christopher chute.
Abstract

4:50 63 Application of text mining and semantic technology in external intelligence surveillance

Yiqun H Li, lihy@lilly.com,
Abstract

5:20   Concluding Remarks

Monday, September 9, 2013

Sci-Mix - EVE Session
Indiana Convention Center
Room: Halls F&G
Jeremy Garritano, Organizers
, Presiding
8:00 pm - 10:00 pm
  9 ChemDraw, iPads, and collaboration tools in the classroom: Results of a joint PerkinElmer and McGraw Hill pilot at the organic chemistry undergraduate level

Robin Y Smith1, robin.smith@perkinelmer.com, Hans C Keil1, hans.keil@perkinelmer.com, Tamara Hodge2.
Abstract

12 Enabling chemistry on-the-go with modern solutions

Tamsin E Mansley1, tamsin.mansley@dotmatics.com, Graeme E Dennis1, Shikha O'Brien2.
Abstract

15 Improving access to data: A distributed approach

Graeme E Dennis1, graeme.dennis@dotmatics.com, Tamsin E Mansley1, Shikha O'Brien2.
Abstract

22 OPSIN: Taming the jungle of IUPAC chemical nomenclature

Daniel M Lowe, daniel@nextmovesoftware.com, Peter Murray-Rust, Robert C Glen.
Abstract

26 Molecular scaffolds are special and useful guides to discovery

Jeremy J Yang1,2, jjyang@salud.unm.edu, Cristian G Bologa1, David J Wild2, Tudor I Oprea1.
Abstract

29 Enhanced ranking of PknB inhibitors using data fusion methods

Abhik Seal, abseal@indiana.edu, David John Wild.
Abstract

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

Ahmed El Kerdawy1, ahmed.elkerdawy@chemie.uni-erlangen.de, Stefan Güssregen2, Hans Matter2, Matthias Hennemann1,3, Timothy Clark1,3,4.
Abstract

62 Standardized drug and pharmacological class network in ontology representation

Qian Zhu, zhu.qian@mayo.edu, Cui Tao, Christopher chute.
Abstract

64 Teach-Discover-Treat: Round 2 competitions

Rommie E Amaro1, ramaro@ucsd.edu, Johanna Jansen2, Jane Tseng4, Wendy Cornell3.
Abstract

66 Adventures in drug discovery: For now we see through a glass, darkly

Robert C Glen, rcg28@cam.ac.uk,
Abstract

83 Teaching information literacy through an undergraduate laboratory project

Martin A Walker, walkerma@potsdam.edu,
Abstract

85 Designing instruction activities to guide students through the research lifecycle: A science librarian approach

Ye Li, liye@umich.edu,
Abstract

87 Anything BUT overlooked: Librarians teaching scientific communication skills at the University of Florida

Donna T. Wrublewski1, dtwrublewski@library.caltech.edu, Amy Buhler2, Sara Gonzalez2, Margeaux Johnson2.
Abstract

92 HPCC: A suitable solution for performing drug repositioning and preclinical pharmacological profiling

Arnaud Sinan Karaboga1, karaboga@harmonicpharma.com, Florent Petronin1, Michel Souchet1, Bernard Maigret2.
Abstract

93 GES polypharmacology fingerprints: A novel and powerful drug repositioning tool

Violeta I. Perez-Nueno1, pereznueno@harmonicpharma.com, Arnaud S. Karaboga1, Michel Souchet1, Dave Ritchie2.
Abstract

96 WITHDRAWN
112 Extraction, analysis, atom-mapping, classification, and naming of reactions from pharmaceutical ELNs

Roger Sayle, roger@nextmovesoftware.com, Daniel Lowe, Noel O'Boyle.
Abstract

117 Chemotype approach to mapping the chemical landscape and exploring chemical-biological interactions within EPA's ToxCast project

Rachelle J Bienstock1, bienstock.rachelle@epa.gov, Chihae Yang2, Jim Rathman2, Ann M Richard3.
Abstract

Tuesday, September 10, 2013

Herman Skolnik Award Symposium - AM Session
Indiana Convention Center
Room: 140
Richard Cramer, Organizers
Brian Masek, Presiding
8:30 am - 11:50 am
8:30   Introductory Remarks
8:35 65 Adventures in CoMFAland

Robert D Clark, bob@simulations-plus.com,
Abstract

9:05 66 Adventures in drug discovery: For now we see through a glass, darkly

Robert C Glen, rcg28@cam.ac.uk,
Abstract

9:35 67 Three paradigm shifts in computer-assisted drug design: The inventors and by-standers

Yvonne C Martin, yvonnecmartin@comcast.net,
Abstract

10:05   Intermission
10:20 68 Look back at 3D-QSAR and Dick Cramer

Anton J. Hopfinger, hopfingr@gmail.com,
Abstract

10:50 69 Evolution of QSAR from regression analysis to physical modeling

Ajay N Jain, ajain@jainlab.org,
Abstract

11:20 70 Scientific analysis of baseball performance

David W. Smith, dwsmith@retrosheet.org,
Abstract

Tuesday, September 10, 2013

Herman Skolnik Award Symposium - PM Session
Indiana Convention Center
Room: 140
Richard Cramer, Organizers
Terry Stouch, Presiding
2:00 pm - 4:45 pm
2:00   Introductory Remarks
2:05 71 Synthesis planning: Something about reactions, representation, relationships, and reasoning

W. Todd Wipke, wipke@ucsc.edu,
Abstract

2:35 72 Think local, act global: Some challenges in cheminformatics and drug research

Tudor I Oprea, toprea@salud.unm.edu,
Abstract

3:05   Intermission
3:20 73 From library design to off-target prediction: A wide array of topomer applications

Bernd Wendt, bernd.wendt@certara.com,
Abstract

3:50 74 Whole template CoMFA: The QSAR grail?

Richard D Cramer, cramer@tripos.com,
Abstract

4:35   Award Presentation

Wednesday, September 11, 2013

Exchangeable Molecular and Analytical Data Formats and their Importance in Facilitating Data Exchange - AM Session Exchanging Molecular Data
Indiana Convention Center
Room: 140
Cosponsored by COMP
Antony Williams, Robert Lancashire, Organizers
Antony Williams, Presiding
8:05 am - 12:00 pm
8:05   Introductory Remarks
8:10 75 Cheminformatics runs on molfiles and its siblings: There is a molfile for that

Keith T Taylor, keith.taylor@accelrys.com,
Abstract

8:40 76 Reading and writing molecular file formats for data exchange of small molecules, biopolymers, and reactions

Roger A Sayle, roger@nextmovesoftware.com,
Abstract

9:10   Intermission
9:20 77 Facilitating accurate chemical data interconversion using Open Babel: The good, the bad, and the painful

Geoffrey R Hutchison, geoffh@pitt.edu,
Abstract

9:50 78 Exchanging chemical structures and ELN data: CDX, CDXML, and other formats

David Gosalvez, Alex Jewett, Phil McHale, phil.mchale@perkinelmer.com, Churl Oh, Rudy Potenzone, rudy.potenzone@perkinelmer.com, Chris Strassel.
Abstract

10:20 79 InChI: Recent developments in the worldwide chemical structure identifier standard

Stephen Heller, steve@hellers.com,
Abstract

10:50   Intermission
11:00 80 Data exchange caveats and particulars, the devil is in the details

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

11:30 81 Pistoia Alliance and the emerging HELM standard at the “dawn of the ADC informatics era”

Sergio Rotsein1,2, John Wise1,3, Claire Ballamy1, Michael Braxenthaler1,4, Barry Bunin1,5, bbunin@collaborativedrug.com.
Abstract

Wednesday, September 11, 2013

Before and After Lab: Instructing Students in 'Non-Chemical' Research Skills - AM Session
Indiana Convention Center
Room: 141
Cosponsored by CHED, YCC
Andrea Twiss-Brooks, Charles Huber, Organizers
Charles Huber, Presiding
8:10 am - 12:00 pm
8:10   Introductory Remarks
8:15 82 Chemical information across San Diego County: A community college and university library collaboration for an independent synthesis project

Teri M Vogel1, tmvogel@ucsd.edu, Cynthia B Gilley2.
Abstract

8:45 83 Teaching information literacy through an undergraduate laboratory project

Martin A Walker, walkerma@potsdam.edu,
Abstract

9:15 84 Integrating citations as a teaching element into chemistry information literacy training sessions

Shu Guo, guo1s@cmich.edu,
Abstract

9:45   Intermission
10:00 85 Designing instruction activities to guide students through the research lifecycle: A science librarian approach

Ye Li, liye@umich.edu,
Abstract

10:30 86 "I can just copy this, right?": Introducing students to copyright

Charles F. Huber, huber@library.ucsb.edu,
Abstract

11:00 87 Anything BUT overlooked: Librarians teaching scientific communication skills at the University of Florida

Donna T. Wrublewski1, dtwrublewski@library.caltech.edu, Amy Buhler2, Sara Gonzalez2, Margeaux Johnson2.
Abstract

11:30 88 Introducing Electronic Laboratory Notebooks (ELNs) to students and researchers at the University of Maryland College Park

Svetla Baykoucheva1, sbaykouc@umd.edu, Lee Friedman2.
Abstract

Wednesday, September 11, 2013

Computational Profiling and Repositioning as Promising New Ways of Drug Development - AM Session
Indiana Convention Center
Room: 142
Cosponsored by COMP
Andrew Hopkins, Violeta Isabel Perez Nueno, Organizers
Violeta Isabel Perez Nueno, Presiding
8:00 am - 12:15 pm
8:00   Introductory Remarks
8:05 89 Actual and predicted target and activity profiles for pharmaceuticals

John P Overington, jpo@ebi.ac.uk,
Abstract

8:30 90 Ligand promiscuity or protein redundancy?: Lessons from the PDB

Esther Kellenberger, ekellen@unistra.fr, Noé Sturm, Jérémy Desaphy, Didier Rognan.
Abstract

8:55 91 Predicting and testing drug off- and on-targets

Brian Shoichet, bshoichet@gmail.com,
Abstract

9:20   Intermission
9:30 92 HPCC: A suitable solution for performing drug repositioning and preclinical pharmacological profiling

Arnaud Sinan Karaboga1, karaboga@harmonicpharma.com, Florent Petronin1, Michel Souchet1, Bernard Maigret2.
Abstract

9:55 93 GES polypharmacology fingerprints: A novel and powerful drug repositioning tool

Violeta I. Perez-Nueno1, pereznueno@harmonicpharma.com, Arnaud S. Karaboga1, Michel Souchet1, Dave Ritchie2.
Abstract

10:20 94 Polypharmacology computational tools: Machine learning with Bayesian classifiers

Jeremy L Jenkins, jeremy.jenkins@novartis.com,
Abstract

10:45   Intermission
10:55 95 Effect and target profile prediction by interaction pattern based drug design

Zoltan Simon1,2, Agnes Peragovics3, Laszlo Vegner3, Balazs Jelinek1,4, Peter Hari1,2, Istvan Bitter1,5, Pal Czobor1,5, Andras Malnasi-Csizmadia1,3,4, malnalab@yahoo.com.
Abstract

11:20 96 Drug repositioning for discovery of novel TRAF2 and NCK-interacting kinase (TNIK) inhibitors

Lu Chen, LChen8@mdanderson.org, Shuxing Zhang.
Abstract

11:45 97 Structure-based discovery of prescription drugs that interact with Solute Carrier (SLC) transporters

Avner Schlessinger, avner.schlessinger@mssm.edu,
Abstract

12:10   Concluding Remarks

Wednesday, September 11, 2013

Exchangeable Molecular and Analytical Data Formats and their Importance in Facilitating Data Exchange - PM Session Exchanging Analytical Data
Indiana Convention Center
Room: 140
Cosponsored by COMP
Antony Williams, Robert Lancashire, Organizers
Robert Lancashire, Presiding
1:30 pm - 4:15 pm
1:30 98 30 years of JCAMP-DX formats and still going strong

Antony N Davies1, Robert J Lancashire2, robert.lancashire@uwimona.edu.jm.
Abstract

2:00 99 Knowledge sharing or what I learned in first grade

Michael Boruta, michael.boruta@acdlabs.com,
Abstract

2:30 100 Long wait for exchangeable data formats vs. the evolution of data

Clemens Anklin, Clemens.Anklin@bruker-biospin.com,
Abstract

3:00   Intermission
3:10 101 Leveraging the AnIML specification for analytical data exchange

Stuart J Chalk, schalk@unf.edu,
Abstract

3:40 102 JCAMP-MOL: A JCAMP-DX extension to allow interactive model/spectrum exploration using Jmol and JSpecView

Robert M Hanson1, hansonr@stolaf.edu, Robert J Lancashire2.
Abstract

4:10   Concluding Remarks

Wednesday, September 11, 2013

Before and After Lab: Instructing Students in 'Non-Chemical' Research Skills - PM Session
Indiana Convention Center
Room: 141
Cosponsored by CHED, YCC
Andrea Twiss-Brooks, Charles Huber, Organizers
Charles Huber, Presiding
1:00 pm - 3:05 pm
1:00   Introductory Remarks
1:05 103 Teaching chemical information in bulk: Incorporating information skills in a large laboratory class

Judith N. Currano, currano@pobox.upenn.edu,
Abstract

1:35 104 Social profile of a chemist online: The potential profits of participation

Antony J Williams, williamsa@rsc.org,
Abstract

2:05 105 Safety outreach to the academic chemistry community

Ralph Stuart, rstuart@cornell.edu,
Abstract

2:35 106 Other skills for post-graduates

Pamela J Scott, pamela.j.scott@pfizer.com,
Abstract

Wednesday, September 11, 2013

Back to the Future: Print Resources in a Digital World - PM Session
Indiana Convention Center
Room: 141
Grace Baysinger, Organizers
Grace Baysinger, Presiding
3:10 pm - 5:30 pm
3:10   Introductory Remarks
3:15 107 Digitizing documents to provide a public spectroscopy database

Antony J Williams1, williamsa@rsc.org, Colin Batchelor2, William Brouwer3, Valery Tkachenko1.
Abstract

3:45 108 Whither the books? Managing access to print resources in an academic elibrary

Leah R McEwen, lrm1@cornell.edu,
Abstract

4:15   Intermission
4:30 109 Keeping the books on campus: The University of Chicago approach to library collection

Andrea Twiss-Brooks, atbrooks@uchicago.edu,
Abstract

5:00 110 Challenges and opportunities for academic research chemistry collections in the 21st century

Grace Baysinger, graceb@stanford.edu,
Abstract

Thursday, September 12, 2013

Exchangeable Molecular and Analytical Data Formats and their Importance in Facilitating Data Exchange - AM Session Data Standards to Support Publishing and Lab Notebooks
Indiana Convention Center
Room: 140
Cosponsored by COMP
Antony Williams, Robert Lancashire, Organizers
Robert Lancashire, Presiding
9:05 am - 10:40 am
9:05   Introductory Remarks
9:10 111 Importance of standards for data exchange and interchange on the Royal Society of Chemistry eScience platforms

Antony J. Williams1, williamsa@rsc.org, Colin Batchelor2, Jon Steele2, Valery Tkachenko1.
Abstract

9:40 112 Extraction, analysis, atom-mapping, classification, and naming of reactions from pharmaceutical ELNs

Roger Sayle, roger@nextmovesoftware.com, Daniel Lowe, Noel O'Boyle.
Abstract

10:10 113 How standards helped RSC to create The Merck Index Online

Richard Kidd, kiddr@rsc.org,
Abstract

Thursday, September 12, 2013

Exchangeable Molecular and Analytical Data Formats and their Importance in Facilitating Data Exchange - AM Session Data Exchange Standards in Chemistry and Drug Discovery
Indiana Convention Center
Room: 140
Cosponsored by COMP
Antony Williams, Robert Lancashire, Organizers
Antony Williams, Presiding
10:55 am - 12:00 pm
10:55 114 Practical open data exchange formats for open organic chemistry projects

Jean-Claude Bradley1, bradlejc@drexel.edu, Andrew SID Lang2, Antony J Williams3.
Abstract

11:25 115 Semantic mining and prediction for drug discovery

Bin Chen1, Bing He3, Ying Ding2, dingying@indiana.edu, David Wild2.
Abstract

11:55   Concluding Remarks

Thursday, September 12, 2013

General Papers - PM Session
Indiana Convention Center
Room: 140
Jeremy Garritano, Organizers
Jeremy Garritano, Presiding
1:00 pm - 2:30 pm
1:00 116 Eureka Research Workbench: A semantic approach to an open source electronic laboratory notebook

Stuart J Chalk, schalk@unf.edu,
Abstract

1:30 117 Chemotype approach to mapping the chemical landscape and exploring chemical-biological interactions within EPA's ToxCast project

Rachelle J Bienstock1, bienstock.rachelle@epa.gov, Chihae Yang2, Jim Rathman2, Ann M Richard3.
Abstract

2:00 pm 118 WITHDRAWN

CHAS, Linda Stroud, Debbie Decker Sunday, September 8, 2013

New Horizons in Chemical Health and Safety - PM Session
Indiana Convention Center
Room: 115
Cosponsored by CCS, CINF
Ralph Stuart, Organizers
Ralph Stuart, Presiding
2:50 pm - 6:40 pm
2:50   Introductory Remarks
2:55 4 Change is the only constant
Kenneth P. Fivizzani
3:15 5 How the CPT can help safety take its rightful place in the chemistry curriculum
David C Finster
3:35 6 Shifting from specific subject-matter experts to all-hazards' safety outreach staff in EHS
Erik A Talley
3:55   Intermission
4:05 7 New horizons, lessons from the Nanotechnology Research Center: Understanding and managing laboratory health and safety of a new or emerging technology
Laura L Hodson, Charles Geraci.
4:25 8 New horizons, emerging technologies, converging safety cultures? Learning from the challenges of nanotechnology
Charles Geraci, Laura Hodson.
4:45 9 Providing environmental, health and safety support for multi-institutional collaborations
Kimberly B Jeskie
5:05   Intermission
5:15 10 Lab safety training in a Web 2.0 world
Ralph Stuart
5:35 11 Accessing chemical health and safety data online using Royal Society of Chemistry resources
Antony J. Williams, Colin Batchelor, Alexey Pshenichnov, Valery Tkachenko.
5:55 12 Impact of new information sharing and retrieval mechanisms on the assessment of chemical safety
Jean-Claude Bradley
6:15 13 Encouraging a culture of safety through educational technology: Developing tools for the 21st century
Ken B Smith, John G Palmer, Debbie M Decker.
6:35   Concluding Remarks

COMP, Emilio Esposito, Scott Wildman Sunday, September 8, 2013

20 Years of PME: Symposium in Honor of Tom Darden, Lee G. Pedersen, and Darrin York - AM Session
Indiana Convention Center
Room: 137
Cosponsored by BIOL, CINF, MEDI, PHYS
Gerardo Cisneros, Jean-Philip Piquemal, Celeste Sagui, Organizers
Gerardo Cisneros, Tamar Schlick, Presiding
8:30 am - 11:45 am
8:30   Introductory Remarks
8:35 13 Modeling halogen compounds with a polarizable multipole force field
Pengyu Ren, Xiaojia Mu, Qiantao Wang, Lee-Ping Wang.
9:05 14 Testing long-range allostery with molecular dynamics
Lee G. Pedersen, Sang W Wu, Chang J Lee.
9:35 15 Tales from a member of the PME generation: From QM/MM to GPUs
Ross C Walker
10:05   Intermission
10:15 16 Molecular insights into ribonucleotide insertion using molecular dynamics simulations
Lalith Perera
10:45 17 Simulations of nucleic acids and/or how PME changed my life
Thomas E. Cheatham
11:15 18 PME on the Big Iron, T3D to GPU and beyond
Michael F Crowley

COMP, Emilio Esposito, Scott Wildman Sunday, September 8, 2013

20 Years of PME: Symposium in Honor of Tom Darden, Lee G. Pedersen, and Darrin York - PM Session
Indiana Convention Center
Room: 137
Cosponsored by BIOL, CINF, MEDI, PHYS
Celeste Sagui, Gerardo Cisneros, Jean-Philip Piquemal, Organizers
Pengyu Ren, Ross Walker, Presiding
1:30 pm - 4:45 pm
1:30 47 Protein structure refinement with a polarizable force field and PME
Stephen LuCore, Jooyeon Park, Kyle Powers, Shuxiang Li, Timothy D Fenn, Michael J Schnieders.
2:00 48 Atomistic dynamics simulations of DNA polymerase conformational pathways help unravel mechanistic aspects of enzyme repair
Yunlang Li, Tamar Schlick.
2:30 49 All-atom simulations of biomolecular crystals
David A Case
3:00   Intermission
3:15 50 Insights into DNA packaging and gene expression revealed from computer simulation
Wilma K Olson
3:45 51 Pocket full of promise: Simulation-based discovery against p53
Rommie E Amaro
4:15 52 High resolution reversible folding simulations of hyperstable RNA tetraloops
Alan A Chen, Angel E Garcia.

COMP, Emilio Esposito, Scott Wildman Monday, September 9, 2013

20 Years of PME: Symposium in Honor of Tom Darden, Lee G. Pedersen, and Darrin York - AM Session
Indiana Convention Center
Room: 137
Cosponsored by BIOL, CINF, MEDI, PHYS
Celeste Sagui, Gerardo Cisneros, Jean-Philip Piquemal, Organizers
David Case, Jean-Philip Piquemal, Presiding
8:30 am - 11:45 am
8:30 78 On the numerical accuracy of Ewald, smooth particle mesh Ewald, and staggered mesh Ewald methods for inhomogeneous and correlated molecular systems
Han Wang, Pingwen Zhang, Christof Schütte.
9:00 79 Particle-mesh Ewald summation for long-range electrostatics in biomolecular simulations: How important are long-range electrostatics corrections?
Terry P Lybrand
9:30 80 Recent Ewald techniques for the efficient calculation of multipole moment interactions and complex QM/MM systems
Bernard R. Brooks, Yihan Shao, Frank C. Pickard, Andrew Simmonett.
10:00   Intermission
10:15 81 GEM: A new force field that combines GEM and AMOEBA
Oleg Starovoytov, Robert G. Duke, Pengyu Ren, Jean-Philip Piquemal, G. Andrés Cisneros.
10:45 82 Linear scaling density functional tight binding models
Timothy J Giese, Darrin M York, Erich Kuechler.
11:15 83 Systematic improvement on the classical molecular model of water
Lee-Ping Wang, Teresa Head-Gordon, Jay W. Ponder, Pengyu Ren, John D. Chodera, Peter K. Eastman, Todd J. Martinez, Vijay S. Pande.

COMP, Emilio Esposito, Scott Wildman Monday, September 9, 2013

20 Years of PME: Symposium in Honor of Tom Darden, Lee G. Pedersen, and Darrin York - PM Session
Indiana Convention Center
Room: 137
Cosponsored by BIOL, CINF, MEDI, PHYS
Celeste Sagui, Gerardo Cisneros, Jean-Philip Piquemal, Organizers
Celeste Sagui, Michael Schnieders, Presiding
1:30 pm - 4:45 pm
1:30 110 Electrostatics in the AMOEBA force field: The long and the short of it
Jay W Ponder
2:00 111 Electrostatic interactions in simulations of nucleic acids
Darrin M York
2:30 112 Non-equilibrium free energy methods for biomolecular simulations
Celeste Sagui, Volodymyr Babin, Mahmoud Moradi, Christopher Roland.
3:00   Intermission
3:15 113 Adding penetration effects to particle mesh Ewald using damping functions
Christophe Narth, Pengyu Y Ren, G. Andrés Cisneros, Jean-Philip PIQUEMAL.
3:45 114 Periodic boundary conditions in molecular simulations
Gerhard Hummer
4:15 115 Treatment of long range dispersion interactions
Tom A Darden

COMP, Emilio Esposito, Scott Wildman Tuesday, September 10, 2013

Developments in Systems Chemical Biology - PM Session
Indiana Convention Center
Room: 136
Cosponsored by CINF, MEDI
Jeffrey Sutherland, Organizers
Jeffrey Sutherland, Michal Vieth, Presiding
1:30 pm - 5:45 pm
1:30 166 Reconstruction and data-mining of assay cascades from literature bioactivity data
John P Overington
2:00 167 AbbVie polypharmacology explorer: A belief theory approach to constructing and querying chemical biology networks
Steven W Muchmore, James T Metz, Phillip J Hajduk.
2:30 168 What can we learn from profiling and predictive data – implications to target space and selectivity assessment
Michal Vieth, Cen Gao, Jibo Wang, Sutherland Jeffrey, Suntara Cahya, Ian Watson, Christos Nicolaou, Thibault Varin.
3:00 169 Network-focused chemogenomics in phenotypic HTS
Jeremy L Jenkins
3:30   Intermission
3:45 170 Exploring a structural protein-drug interactome for chemical probes and therapeutics in cancer
Samy Meroueh
4:15 171 New systems pharmacology approach toward better adverse drug response predictions
Jake Chen
4:45 172 Applied Systems Chemical Biology and the quest for novel agents against tuberculosis
Tudor I Oprea, Andrei Leitao, Elebeoba E May, Alexander Tropsha.
5:15 173 Chemo-evolutionary basis of polypharmacology
Brian K Shoichet

COMP, Emilio Esposito, Scott Wildman Monday, September 9, 2013

Drug Discovery - PM Session We Seek Information to Solve our #structuralBioinformatics and #target-basedDesign Ponderings #drugDisco
Indiana Convention Center
Room: 136
Cosponsored by BIOL, CINF, MEDI
Scott Wildman, Y. Jane Tseng, Organizers
Y. Jane Tseng, Presiding
1:30 pm - 5:15 pm
1:30 103 Design of antiandrogens: Challenge of receptor modeling
Anton Filikov, Antonella Pepe, Vineet Kumar, Sanjay V Malhotra.
2:00 104 Impact of inhibitors on the tertiary structure of acetylcholinesterase
Emilio Xavier Esposito, Terry R Stouch, Troy Wymore, Jeffry D Madura.
2:30 105 Structure-based function prediction for proteins of unknown function employing ProBiS enhanced by molecular dynamics
Dusanka Janezic
3:00 106 Molecular dynamics studies of the role of protein flexibility in immunological molecular recognition
Cory M Ayres, Daniel R Scott, Brian M Baker, Steven A Corcelli.
3:30   Intermission
3:45 107 Structure-based discovery of human asparagine synthetase inhibitors
Lamees S. Hegazy, Nigel G.J. Richards.
4:15 108 Searching with statistics: Is pose prediction perfectible?
Paul Hawkins
4:45 109 Progress towards an integrated structural informatics and SBDD desktop tool
Jibo Wang, Hongzhou Zhang, Cen Gao, Carlos Perez, Abdelaziz Mahoui, Christine Humblet, Michal Vieth, Jon A Erickson.

COMP, Emilio Esposito, Scott Wildman Tuesday, September 10, 2013

Drug Discovery - AM Session It's What You do with the Information... #StructuralBioinformatics #Target-basedDesign #drugDisco #
Indiana Convention Center
Room: 136
Cosponsored by BIOL, CINF, MEDI
Scott Wildman, Y. Jane Tseng, Organizers
Terry Stouch, Presiding
8:30 am - 11:45 am
8:30 136 Identification of allosteric Akt inhibitors by computational methods
Oya Gursoy, Elif Ozkirimli, Kutlu O Ulgen.
9:00 137 Characterizing an evolved CXC chemokine receptor interface
Sara E Nichols, Carlos X Hernández, Yi Wang, J. Andrew McCammon.
9:30 138 Virtual screening of PERK inhibitors
Qiantao Wang, Jihyun Park, Ashiwini Devkota, Kevin N Dalby, Pengyu Ren.
10:00   Intermission
10:15 139 Structure-based design of macrocyclic kinase inhibitors
Anders Poulsen, Anthony D Wiliam, Steephanie Blanchard, Brian Dymock.
10:45 140 Structure-based design of LpxC inhibitors selective against histone deacetylase
Matthew D Miller, Pamela Hill, Moriah Gagnon, Tyler Grebe, Allison Choy, Kerry Benenato, Valerie Marone, Philip Ross, Michael Hale.
11:15 141 Automation of Monte Carlo relative free energy calculations for ligand design
Julien Michel, Hannes Loeffler, Christopher Woods.

COMP, Emilio Esposito, Scott Wildman Wednesday, September 11, 2013

Drug Discovery - AM Session It's not @acsCOMP without a Little #methodMadness! #drugDisco Style
Indiana Convention Center
Room: 136
Cosponsored by BIOL, CINF, MEDI
Scott Wildman, Y. Jane Tseng, Organizers
Ryan Coleman, Presiding
8:30 am - 11:45 am
8:30 276 2D replica-exchange method for the prediction of protein-ligand binding structures
Hironori Kokubo, Toshimasa Tanaka, Yuko Okamoto.
9:00 277 Comprehensive validation of a computational docking methodology to identify the noncovalent binding site of a ligand to DNA
Christos Deligkaris, Anthony T. Ascone, Kevin J. Sweeney.
9:30 278 Virtual screening: Worse than failure
Scott A. Wildman
10:00   Intermission
10:15 279 Remotely guided chemical synthesis system for discovery chemistry
Mark A Vincent, Alexander G Godfrey, Jeffrey D Gygi.
10:45 280 Racemization: An integrated experimental-quantum mechanical-informatics approach
Andrew G Leach
11:15 281 New computational approaches to design of a highly efficient therapeutic enzyme for treatment of cocaine abuse
Fang Zheng, Liu Xue, Shurong Hou, Wenchao Yang, Max Zhan, Chang-Guo Zhan.

COMP, Emilio Esposito, Scott Wildman Thursday, September 12, 2013

Drug Discovery - AM Session Analyzing the Chemical and Structural Information for #drugDisco Keeps You Ahead of the Rest. Not Really Sure who the Rest are...
Indiana Convention Center
Room: 136
Cosponsored by BIOL, CINF, MEDI
Scott Wildman, Y. Jane Tseng, Organizers
Magdalena Korczynska, Presiding
8:30 am - 11:45 am
8:30 342 WITHDRAWN
9:00 343 P450 site of metabolism predictions using specialized atomic and molecular descriptors with neural network modeling
Jed M Zaretzki, Matt K Matlock, S. Joshua Swamidass.
9:30 344 PubChem structure-activity relationship (SAR) clusters
Sunghwan Kim, Lianyi Han, Evan E Bolton, Stephen H Bryant.
10:00   Intermission
10:15 345 Matched pair generation and application for SAR browsing
Yongjin Xu, Johanna Jansen.
10:45 346 Finding and using activity cliffs in 3D: Gaining more SAR information during lead optimization
Tim Cheeseright, Rae Lawrence, Mark Mackey, Martin Slater.
11:15 347 MP-NSGs: Multiple-property based network-like similarity graphs
Marian R Brodney, Steven D Heck, Jared J Milbank, Preeti Iyer, Dilyana Dimova, Jürgen Bajorath, Veerabahu Shanmugasundaram.

COMP, Emilio Esposito, Scott Wildman Sunday, September 8, 2013

Emerging Technologies in Computational Chemistry - PM Session
Indiana Convention Center
Room: 136
Cosponsored by BIOL, CINF, MEDI, PHYS
Curtis Breneman, Organizers
Curtis Breneman, Presiding
1:30 pm - 4:55 pm
1:30   Introductory Remarks
1:35 40 Objective models for ligand binding characteristics from quantum mechanics
Timothy Clark
2:00 41 Beyond the scope of Free-Wilson analysis: Building interpretable QSAR models with machine learning algorithms
Hongming Chen, Ingemar Nilsson, Lars Carlsson, Mats Eriksson, Peter Varkonyi, Ulf Norinder.
2:25 42 ForceBalance, a method for developing better force fields
Lee-Ping Wang, Troy Van Voorhis, Todd J. Martinez, Vijay S. Pande.
2:50   Intermission
3:05 43 Estimating classification confidence for ensemble models
Robert D Clark, Wenkel Liang, Marvin Waldman, Robert Fraczkiewicz.
3:30 44 Catching transition states by throwing ropes to stable intermediates
Paul Zimmerman
3:55 45 Beyond comparison of two structures: Using machine learning to quantify changes in molecular motion
Sameer Varma
4:20 46 Computational design of a highly efficient enzyme
Fang Zheng, Liu Xue, Shurong Hou, Wenchao Yang, Junjun Liu, Chang-Guo Zhan.
4:45   Award Presentation

COMP, Emilio Esposito, Scott Wildman Tuesday, September 10, 2013

Expanding Computational Chemistry with GPUs - AM Session
Indiana Convention Center
Room: 137
Cosponsored by BIOL, CINF, MEDI, PHYS
Kenneth Merz, Scott Le Grand, Organizers
, Presiding
8:30 am - 11:20 am
8:30   Introductory Remarks
8:35 am 142 WITHDRAWN
9:05 143 Multireference coupled cluster methods on heterogeneous CPU-GPU systems
Kiran Bhaskaran-Nair, Wenjing Ma, Sriram Krishnamoorthy, Oreste Villa, Hubertus JJ van Dam, Edoardo Apra, Karol Kowalski.
9:35 144 Super Instruction Architecture for petascale computing on heterogeneous systems
Beverly A Sanders, Nakul Jindal, Victor Lotrich, Erik Deumens.
10:05   Intermission
10:20 145 Quantum chemistry many-body methods on multicore processors and accelerators
Eugene DePrince, Jeff Hammond.
10:50 146 Interactive ab initio molecular dynamics
Nathan Luehr, Alex Jin, Todd J Martinez.

COMP, Emilio Esposito, Scott Wildman Tuesday, September 10, 2013

Expanding Computational Chemistry with GPUs - PM Session
Indiana Convention Center
Room: 137
Cosponsored by BIOL, CINF, MEDI, PHYS
Kenneth Merz, Scott Le Grand, Organizers
Kenneth Merz, Scott Le Grand, Presiding
1:30 pm - 4:20 pm
1:30   Introductory Remarks
1:35 174 Apples vs. oranges or apples vs. apples? A comparison of the real-time, real-space elecronic structure approach vs. the Gaussian basis set method using general purpose graphics processing units (GPU)
Alan Aspuru-Guzik
2:05 175 GPU-enabled molecular dynamics on desktop: From the classical to reactive force field
Xiaoxia Li, Mo Zheng, Jian Liu, Zhongliang Liu, Xiaofang Tao, Li Guo.
2:35 176 Acceleration of electron repulsion integral evaluation on graphics processing units via use of recurrence relations
Yipu Miao, Kenneth M Merz.
3:05   Intermission
3:20 177 Accelerating ab initio QM/MM computations using a Supercharger QM module
Kevin J. Naidoo, Kyle Fernandes, Alicia Renison.
3:50 178 Novel codes for quantum chemistry
Mark S Gordon, Andrey Asadchev, Sarom S Leang.

COMP, Emilio Esposito, Scott Wildman Wednesday, September 11, 2013

Expanding Computational Chemistry with GPUs - AM Session
Indiana Convention Center
Room: 137
Cosponsored by BIOL, CINF, MEDI, PHYS
Kenneth Merz, Scott Le Grand, Organizers
Kenneth Merz, Scott Le Grand, Presiding
8:30 am - 11:45 am
8:30 282 Unlikely symbiosis: How supercomputing and gaming are evolving together
Sarah Tariq
9:00 283 Biological sequence alignment with GPU-BLAST
Tianluo Chen, Nick Sahinidis, Panos Vouzis.
9:30 284 GAME: Gpu accelerated mixture elucidator
Yufeng Jane Tseng, Alioune Schurz.
10:00   Intermission
10:15 285 Simulating millisecond dynamics in all-atom detail using a GPU cluster: Protein folding and conformational change of kinases and GPCRs
Vijay Pande
10:45 286 Impact of Kepler: Molecular dynamics and the GPU revolution
Ross C Walker
11:15 287 Interactive molecular visualization and analysis with GPU computing
John E. Stone

COMP, Emilio Esposito, Scott Wildman Sunday, September 8, 2013

Material Science - AM Session Loving the #matSci research? We are. Follow us on twitter! @acsCOMP
Indiana Convention Center
Room: 136
Cosponsored by CINF, PHYS, PMSE, POLY
Maciej Haranczyk, Organizers
Luke Achenie, Presiding
8:30 am - 11:45 am
8:30 7 Towards the rational design of organic piezoelectric materials
Daniel S Lambrecht, Geoffrey R. Hutchison, Keith A Werling.
9:00 8 Effect of catalysts and solvent on the stereoregularity and kinetics of acrylate derivatives: A computational approach
Viktorya Aviyente, Tugba Furuncuoglu Ozaltin.
9:30 9 Development of a genetic algorithm with applications to heterogeneous nucleation
Geoffrey P. F. Wood, Keith Chadwick, Erik E. Santiso, Bernhardt L. Trout.
10:00   Intermission
10:15 10 Metal-organic frameworks for oxygen-enrichment of air: Insights from molecular simulation
Marie V. Parkes, Jeffery A. Greathouse, Tina M. Nenoff.
10:45 11 Explaining the range of single-molecule aniline conductance measurements: Computational search for high-conductance conformers
Wendu Ding, Christian F. A. Negre, Leslie Vogt, Victor S. Batista.
11:15 12 Oxygen diffusion in nickel: Ab initio calculations in combination with kinetic Monte Carlo approach
Dominic Alfonso

COMP, Emilio Esposito, Scott Wildman Monday, September 9, 2013

Material Science - AM Session The Great Thing about #matSci is its Use of Different Computational Methods #methodMadness
Indiana Convention Center
Room: 136
Cosponsored by CINF, PHYS, PMSE, POLY
Maciej Haranczyk, Organizers
Rebecca Weber, Presiding
8:30 am - 11:45 am
8:30 72 Quantum chemical molecular dynamics study on film growth mechanisms of microcrystalline silicon solar cells
Takuya Kuwahara, Hiroshi Ito, Yuji Higuchi, Nobuki Ozawa, Momoji Kubo.
9:00 73 Combined experimental and theoretical approach to identify crystal structures of new high-pressure polymorphs of FOX-7 crystal
Boris Averkiev, Yuchuan Tao, Santanu Chaudhuri, Zbigniew A Dreger, Yogendra M Gupta.
9:30 74 Controlling the localisation of d- and f- electrons using DFT+U with occupation matrices
Jeremy P Allen, Graeme W Watson.
10:00   Intermission
10:15 75 Defect engineering in Cr2O3: Prospects for the development of a p-type transparent conductive oxide
Aoife B. Kehoe, Graeme W. Watson.
10:45 76 Synthesis of nitrogen: Methane clusters under electron irradiation
Iogann Tolbatov, Sylwia Ptasinska, Daniel M. Chipman.
11:15 77 Efficient chemical space exploration and accelerated property predictions using machine learning
Ghanshyam Pilania, Chenchen Wang, R. Ramprasad.

COMP, Emilio Esposito, Scott Wildman Wednesday, September 11, 2013

Membranes - PM Session @acsCOMPprog Loves a Good Pun but You Won't Find One Here. Just Membranes. All Afternoon #membranes
Indiana Convention Center
Room: 137
Cosponsored by BIOL, CINF, PHYS
Michael Feig, Organizers
Vahid Mirjalili, Presiding
1:30 pm - 5:15 pm
1:30 312 Gating of the calcium release-activated calcium channel: Insights from molecular simulations of the wild type and V174A mutant
Hao Dong, Vincenzo Carnevale, Giacomo Fiorin, Michael L Klein.
2:00 313 Steered molecular dynamics provide insights into the translocation of the cell penetrating peptide pVEC
Begum Alaybeyoglu, Elif Ozkirimli.
2:30 314 Identifying a membrane-dependent pathway for anesthetic binding in ligand-gated ion channels
Mark J Arcario, Emad Tajkhorshid.
3:00 pm 315 WITHDRAWN
3:30   Intermission
3:45 316 Design and development of a special-purpose in silico solvent for modeling lipid-protein interaction in a highly mobile membrane mimetic
Josh V Vermaas, Emad Tajkhorshid.
4:15 pm 317 WITHDRAWN
4:45 318 Efficient numerical Poisson-Boltzmann methods for membrane systems
Wesley M Botello-Smith, Qin M Cai, Ray M Luo.

COMP, Emilio Esposito, Scott Wildman Sunday, September 8, 2013

Molecular Mechanics - AM Session Kicking off #ACSindy with #molMech Applications. Remember to Follow @acsCOMP and @acsCOMPprog
Indiana Convention Center
Room: 139
Cosponsored by BIOL, CINF, MEDI, PHYS
Michael Feig, Organizers
Sara Nichols, Presiding
8:30 am - 11:45 am
8:30 26 Deducing the molecular mechanism of solvation dynamics in imidazolium-based ionic liquids via molecular dynamics simulations
Zack L Terranova, Steven A Corcelli.
9:00 27 Efficient method to elucidate ligand binding pathways: Binding kinetics studies for cryptophane host-guest complexes
Chia-en A. Chang, Christopher C Roberts.
9:30 28 Vibrational energy relaxation in common high energy density materials through reactive molecular dynamics simulations
Mitchell A Wood, Alejandro Strachan.
10:00   Intermission
10:15 29 Molecular dynamics simulations of ionic liquids using improved classical force fields
Yong Zhang, Edward Maginn.
10:45 30 Multiscale modeling of supramolecular assemblies for nanomedical sciences: Applications in computer-aided vaccine design
Harshad Joshi, Abhishek Singharoy, Kristen Lewis, Abhigna Polavarapu, Mu-Hyun Baik, Peter Ortoleva.
11:15 31 Computational predictions of stereoselectivity using Q2MM
Olaf Wiest, Joshua Lee, Aaron Forbes.

COMP, Emilio Esposito, Scott Wildman Monday, September 9, 2013

Molecular Mechanics - AM Session Elecrotstatics and Polarization Help Things Stick Together. Hopefully You'll Stick Around all Morning #molMech
Indiana Convention Center
Room: 139
Cosponsored by BIOL, CINF, MEDI, PHYS
Michael Feig, Organizers
Emilio Esposito, Presiding
8:30 am - 11:45 am
8:30 91 Molecular model of atrazine binding in the QB site of photosystem II
Leslie Vogt, Victor Batista.
9:00 92 Modeling of ligand and HIV-1 protease association by molecular dynamics study
Yu-ming Mindy Huang, Myungshim Kang, Chia-en A Chang.
9:30 93 Mechanisms of configurational transitions and dissociation of a protein-protein complex characterized by all-atom microsecond molecular dynamics simulations
Matthias Buck
10:00   Intermission
10:15 94 Engineering electrostatic control of protein-protein interfaces and chaperone activity
Charles L. Brooks
10:45 95 Evaluation of electrostatic binding free energies in protein-substrate complexes
Jeffry D Madura, Emilio Xavier Esposito.
11:15 96 Control of open–closed conformers of ferric binding proteins by local and environmental perturbations
Canan ATILGAN, Gokce Guven, Ali Rana Atilgan.

COMP, Emilio Esposito, Scott Wildman Tuesday, September 10, 2013

Molecular Mechanics - AM Session Exploring Proteins with #molMech is Part of a Heart Healthy Morning. Not Really. But your Mind will Thank you. #expandYourBrain
Indiana Convention Center
Room: 139
Cosponsored by BIOL, CINF, MEDI, PHYS
Michael Feig, Organizers
Eduardo Sproviero, Presiding
8:30 am - 11:45 am
8:30 154 Understanding of the conformational flexibility of the catalytic α-subunit of human protein kinase CK2
Aurélie Gouron, Hélène Jamet, Anne Milet.
9:00 155 Mechanisms of small molecule binding to intrinsically disordered proteins
Julien Michel, Rémi Cuchillo.
9:30 156 Computational insights for the AlkD base extrusion strategy
Bradley R Kossmann, Ivaylo Ivanov.
10:00   Intermission
10:15 157 Activation mechanism of c-src tyrosine kinase
Diwakar Shukla, Yilin Meng, Benoit Roux, Vijay S. Pande.
10:45 158 Understanding mutation-driven kinase activation of ALK in neuroblastoma patients
Peter J Huwe, Scott C Bresler, Jin H Park, Daniel A Weiser, Yael P Mosse, Mark A Lemmon, Ravi Radhakrishnan.
11:15 159 Molecular mechanism of how palmitate affects the activity of IRE1α/PKR
Liang Fang, Hyunju Cho, Christina Chan, Michael Feig.

COMP, Emilio Esposito, Scott Wildman Wednesday, September 11, 2013

Molecular Mechanics - AM Session Come See if Your Favorite Protein is Part of this #molMech Session!
Indiana Convention Center
Room: 139
Cosponsored by BIOL, CINF, MEDI, PHYS
Michael Feig, Organizers
Monica Berrondo, Presiding
8:30 am - 11:45 am
8:30 294 New structural framework for integrating replication protein A into DNA processing machinery
Chunli Yan, Chris A Brosey, Susan E Tsutakawa, William T Heller, Robert P Rambo, John A Tainer, Walter J Chazin, Ivaylo Ivanov.
9:00 295 Integrative modeling of complex biological asssemblies in transcription
Ivaylo Ivanov
9:30 296 Novel PIP2 lipid binding to focal adhesion kinase probed through coarse-grained molecular dynamics simulations
Jun Feng, Blake Mertz.
10:00   Intermission
10:15 297 Conformational transitions in an ATP-driven calcium pump
Avisek Das, Benoit Roux.
10:45 298 Modeling the effect of length and crowding on the mechanics of microtubule protofilaments
Kelly E. Theisen, Ruxandra I. Dima.
11:15 299 Allosteric coupling of correlated local unfolding and large-amplitude conformational change in proteins
Thomas E Morrell, Ilona Rafalska-Metcalf, Jhih-Wei Chu, Haw Yang.