Technical Program (no abstracts)

ACS Chemical Information Division (CINF)
Fall, 2012 ACS National Meeting
Philadelphia, PA (August 19 - 23)

CINF Symposia

R. Bienstock, Program Chair

SUNDAY MORNING

Philadelphia Marriott Downtown
Room 302/303

When Chemists and Computers Collide: Putting Cheminformatics in the Hands of Medicinal Chemists Cosponsored by MEDI
Matthew Segall, Organizer, Presiding
8:30   Introductory Remarks.
8:35 1 Intersection of chemists, computers, and automation: A fully integrated approach to SAR generation
David M Parry, Christopher N Selway, Willem P Van Hoorn Abstract
9:25 2 Data in, data out - visualization of SAR data organized through an ELN
Anis Khimani, Philip Skinner, Megean Schoenberg, Phil McHale, Michael Swartz, Kate. Abstract
9:35 3 MPO for the masses: Practical application of multiparameter optimisation to guide compound design and selection
Edmund Champness, Matthew Segall, Chris Leeding, James Chisholm, Iskander Yusof Abstract
10:05   Intermission.
10:15 4 Computation tools for medicinal chemists: Increasing the dimensions of drug discovery
Robert Scoffin Abstract
10:45 5 Application of automated and validated virtual screening workflows: A hand-tool for medicinal chemists to generate and/or evaluate ideas
Ferenc Szalai, Márk Sándor, Zoltán Szalai, Gáspár Körtesi, Enikő Dorogi, Róbert Kiss Abstract
11:05 6 Competitive data science: A tale of two web services
David C Thompson, Joerg Bentzien, Ingo Muegge, Ben Hamner Abstract
11:25 7 Putting chemical informatics in the hands of prospective medicinal chemists: QSAR modeling of Plasmepsin II inhibition, an undergraduate project
Jeremy G Frey, Jonathon W Essex, Simon J Cioles Abstract
11:45 8 Better 2D reports for 3D decisions: Communicating with medicinal chemist
Tamsin E Mansley, Krisztina Boda, Bob Tolbert Abstract

 Philadelphia Marriott
Conference Room 307

Science and the Law: Analytical Data in Support of Regulation in Health, Food, and the Environment Cosponsored by AGFD, ANYL, CHAL, ENVR, MEDI, PROF, TOXI
William Town, Organizer, Presiding
8:30   Introductory Remarks.
8:40 9 Honey analysis by high-sensitivity cryo-13C-NMR
Istvan Pelczer Abstract
9:10 10 Ensuring that nutrition and health claims on foods and dietary supplements are justified and scientifically substantiated
David P Richardson. Abstract
9:40   Intermission.
9:55 11 Hunting and gathering: Locating information on the cusp between science and legislation
Judith N. Currano Abstract
10:25 12 Contact lens materials and multipurpose solutions: Lessons learned from laboratory research
K. Scott Phillips, Victoria Hitchins, Dinesh Patwardhan Abstract
10:55 13 Steps towards the analytical standards required for science-based tobacco product regulation
Derek Mariner, Kevin McAdam, Christopher Proctor Abstract

 Philadelphia Marriott
Conferene Room 306

Hunting for Hidden Treasures: Chemical Information in Patents and Other Documents Cosponsored by CHAL, SCHB
Wei Deng, Organizer, Presiding
8:30   Introductory Remarks.
8:35 14 Case studies in Markush searching: Using Markush structures in patents for chemical property description
Donald Walter Abstract
9:00 15 Building pathways to the world's disclosed scientific research
Roger Schenck. Abstract
9:25 16 Natural products Markush
Jayaraman Packirisamy, Yogitha Pathuri. Abstract
9:50   Intermission.
10:00 17 Mission impossible? Computer aided extraction of generic chemical structures from patents: A critical review of the technologies applied and some results of the Theseus project "ChemProspector"
Josef Eiblmaier, Valentina Eigner-Pitto, Hans Kraut, Larisa Isenko, Heinz Saller, Peter Loew Abstract
10:25 18 Chemical text mining for current awareness of pharmaceutical patents
Daniel M Lowe, Roger A Sayle, Paul Hongxing Xie, Sorel Muresan Abstract
10:50   Intermission.
11:05 19 Periscope system for encoding and searching chemical Markush structures
David A Cosgrove, Jon Winter, Andrew G Leach, Andrew Poirrette, Keith M Green Abstract

SUNDAY AFTERNOON

Philadelphia Marriott Downtown
Room 302/303

Cheminformatics and Drug Repurposing
Jose Medina-Franco, Rachelle Bienstock, Organizers
Jose Medina-Franco, Presiding
1:30   Introductory Remarks.
1:35 20 Drug repurposing and multitargeted drug design are the positive faces of failures in reductionist mechanistic drug design
Christopher A Lipinski Abstract
2:00 21 Cheminformatic/bioinformatic mining of large corporate databases for drug repurposing
William Loging, Raul Rodriguez-Esteban, Jon Hill, Thomas Freeman Abstract
2:25 22 Improving drug development by connecting medicinal chemistry with drug repositioning and modern machine learning methods
Iwona E Weidlich, Igor V Filippov, Ian Thorpe Abstract
2:50 23 Mining small-molecule screens to repurpose drugs
S. Joshua J Swamidass Abstract
3:15 24 Diverse valid 3D-QSAR models of off-target effects from template CoMFA
Richard D Cramer Abstract
3:40   Intermission.
3:50 25 Drug design and repositioning using MLSD (multiple ligand simultaneous docking)
Chenglong Li Abstract
4:15 26 Mining public domain data as a basis for drug repurposing
Antony J Williams, Sean Ekins, Valery Tkachenko Abstract
4:40 27 Drug-drug relationship based on target information: Application to drug target identification
Dongsup Kim Abstract
5:05 28 Application of computational target fishing approaches in drug repurposing
Mohamed D AbdulHameed, Anders Wallqvist, Gregory J. Tawa Abstract

 Philadelphia Marriott
Conference Room 307

Science and the Law: Analytical Data in Support of Regulation in Health, Food, and the Environment Cosponsored by AGFD, ANYL, CHAL, ENVR, MEDI, PROF, TOXI
William Town, Organizer, Presiding
1:00   Introductory Remarks.
1:05 29 Rapid screening methods for pharmaceutical surveillance
Lucinda Buhse, Connie M Gryniewicz-Ruzicka, Jamie D Dunn, Sergey Arzhantsev, John A Spencer, Jason Rodriguez, Benjamin J Westenberger, John F Kauffman Abstract
1:35 30 Analytical procedures and the regulation of new drug development
George Lunn Abstract
2:05   Intermission.
2:20 31 Mapping the human toxome for new regulatory tools
Thomas Hartung, Paul Locke Abstract
2:50 32 Cooperation between the US EPA and industry to develop an in vitro ocular hazard testing strategy
Rodger Curren Abstract
3:20 33 Environmental databases: A trip down memory lane and new journeys in the 21st century
Frederick W Stoss Abstract
3:50   Concluding Remarks.

 Philadelphia Marriott
Conferene Room 306

Hunting for Hidden Treasures: Chemical Information in Patents and Other Documents Cosponsored by CHAL, SCHB
Wei Deng, Organizer, Presiding
1:30   Introductory Remarks.
1:35 34 Imago: Open-source toolkit for chemical structure image recognition
Rostislav Chutkov, Michael Rybalkin, Victor Smolov, Kliton Andrea Abstract
2:00 35 Recent developments in the CLiDE tool for extraction of chemical structure data from patents and other documents
Aniko T Valko, Peter Johnson, Vilmos A Valko Abstract
2:25   Intermission.
2:35 36 Advances in automatic chemical spelling correction
Roger A Sayle, Daniel M Lowe Abstract
3:00 37 Automated extraction of structure-activity relationships from chemistry patents
Lutz Weber Abstract
3:25 38 From chaos to order: Collecting chemical and biologic information in the documentation space
Daniel Bonniot de Ruisselet, David Deng Abstract
3:50   Intermission.
4:00 39 Exploring and visualisation of chemistry in patents with Marvin and Instant JChem
Alexander G Klenner Abstract
4:25 40 SureChem: Integrating patent chemistry with public and private nonpatent research resources
Nicko Goncharoff Abstract
4:50 41 Bringing structures to the disorder: Adding chemical intelligence to unstructured documents
Kate Blanchard, Philip Skinner, Phil McHale, Megean Schoenberg, Rudy Potenzone, Scott Flicker, Joshua Wakefiled, Sean Greenhow, Robin Smith Abstract
5:15   Concluding Remarks.

SUNDAY EVENING

Sonesta Hotel Philadelphia,
Room Liberty A

CINF Scholarship for Scientific Excellence
Guenter Grethe, Organizer
6:30 - 8:30
  42 Torsion Fingerprint Deviation: A novel measure to compare small molecule conformations
Christin Schärfer, Tanja Schulz-Gasch, Matthias Rarey, Wolfgang Guba Abstract
  43 Similarity based virtual screening: Effect of the choice of similarity coefficient
Hua Xiang, John Holliday, Peter Willett Abstract
  44 Predicting complex phase behaviour of lyotropic liquid crystals in crystallographic screens
Tu C. Le, Xavier Mulet, Charlotte E. Conn, Frank R. Burden, David A. Winkler Abstract
  45 Prioritization of docking poses in human serotonin and dopamine transporters by the use of common scaffold clustering
Amir Seddik, Barbara Zdrazil, Rene Weissensteiner, Harald H Sitte, Gerhard F Ecker Abstract
  46 Integrated Chemoinformatics approaches to virtual screening in the search of new lead compounds against Leishmania
Rodolpho C. Braga, Luciano M. Lião, José C. B. Bezerra, Marina C. B. Vinaud, Carolina H. Andrade Abstract

MONDAY MORNING

Philadelphia Marriott Downtown
Room 302/303

Future of the History of Chemical Information Cosponsored by HIST
Andrea Twiss-Brooks, Leah Solla, Organizers, Presiding
9:00   Introductory Remarks.
9:05

47

Historical cantilevering
Leah R Solla, Peter F Rusch Abstract
9:20 48 Language and symbolism of chemistry - a historical perspective
William G Town Abstract
9:45 49 Chemical structures
Philip McHale Abstract
10:10   Intermission.
10:20 50 Evolution of computer based structures from WLN to InChI
Stephen Heller Abstract
10:45

51

History of chemical reactions information: Past, present, and future
Guenter Grethe Abstract
11:10   Panel Discussion.

 Philadelphia Marriott
Conference Room 307

Open Notebook Science/Open Chemistry/Electronic Lab Notebook
Philip McHale, Jean-Claude Bradley, Organizer
Jean-Claude Bradley, Presiding
8:30   Introductory Remarks.
8:35

52

Perspective on the market for Electronic Laboratory Notebook technology
Michael H Elliott Abstract
9:05 53 Successful selection and deployment of an ELN throughout a medical university
Cecilia Bjorkdahl Abstract
9:35 54 Getting academic synthetic chemists to use ELNs: Why and how?
Richard J Whitby, Bogdan Ibanescu, Tim Dickens, Brian Brooks Abstract
10:00   Intermission.
10:10 55 Changing role of electronic lab notebooks: How “First To File” is shifting the landscape
Michael Swartz, Philip Skinner, Phil McHale, Alex Jewett, Kate Blanchard Abstract
10:35

56

Leveraging the cloud for partnerships and collaboration
Frederic Bost Abstract
11:00

57

Mobile chemistry apps participating in the open science revolution
Alex M Clark Abstract
11:25

58

Evaluating the quality and performance of automatic atom mapping algorithms
Daniel M Lowe, Roger A Sayle Abstract

MONDAY AFTERNOON

Philadelphia Marriott Downtown
Room 302/303

Future of the History of Chemical Information Cosponsored by HIST
Andrea Twiss-Brooks, Leah Solla, Organizers
Andrea Twiss-Brooks, Presiding
1:00 59 From “Index Chemicus” for chemical documentation to integrated tools for intelligent retrieval
Vijay Bhatia Abstract
1:20 60 Back to the future: CAS and the shape of chemical information to come
Roger Schenck Abstract
1:40 61 How books shape what we know
Bruce V Lewenstein Abstract
2:00 62 Evolution of chemical information instruction
Adrienne W. Kozlowski Abstract
2:20   Intermission.
2:30 63 Looking back, but not in anger: My view of history and future of chemical information
Engelbert Zass Abstract
3:00 64 Data collection in the future: The views and concerns of a historian of chemistry
Jeffrey I. Seeman Abstract
3:20 65 Chemical information: From print to the Internet
Robert E. Buntrock Abstract
3:40   Discussion.

 Philadelphia Marriott
Conference Room 307

Open Notebook Science/Open Chemistry/Electronic Lab Notebook
Jean-Claude Bradley, Philip McHale, Organizers
Jean-Claude Bradley, Presiding
1:15 66 Shining a light on chemical properties with Open Notebook Science and open strategies
Jean-Claude Bradley, Andrew SID Lang Abstract
1:45 67 Leveraging Open Notebook Science for solubility and melting point predictions for optimizing reactions and recrystallizations
Matthew J McBride, Jean-Claude Bradley, William E Acree, Andrew Lang, Antony Williams Abstract
2:05 68 Feeding and consuming data to support Open Notebook Science via the ChemSpider Platform
Antony J Williams, Jean-Claude Bradley, Andrew S.I.D. Lang, Valery Tkachenko Abstract
2:30 69 LabTrove: Software for facilitating open notebook science
Jeremy G Frey Abstract
2:55   Intermission.
3:10 70 Online CHEmical Modeling environment (OCHEM) is an innovative open collaborative platform for chemistry
Iurii Sushko, Sergii Novotarskyi, Robert Körner, Ahmed Abdelaziz, Wolfram Teetz, Igor V. Tetko Abstract
3:30 71 Opening up ELNs and Repositories to support formal publication
Simon J Coles, Graham Tizzard, Jeremy Frey, Andrew Milsted, Mark Edwards, Romanus Onyeabo, John Spencer, Jan Kuras Abstract
3:55 72 ChemWiki: Advancing undergraduate chemistry content, curation, and education with dynamic open-access textbooks
Delmar Larsen Abstract
4:20 73 Negotiating trust in the communication of science by blog
Lawrence Souder Abstract
4:45   CINF Business meeting.

 Hilton Garden Inn Philadelphia
Salon D

Hunting for Hidden Treasures: Chemical Information in Patents and Other Documents Cosponsored by CHAL, SCHB
Wei Deng, Organizer, Presiding
1:00   Introductory Remarks.
1:05 74 Challenges in chemical literature mining
Shashikala G, Anirban Mudi, Lokanath Khamari, Jignesh Bhate Abstract
1:30 75 Where the blue of the night meets the gold of the day: The challenges of collaboration between searcher and client to produce the perfect chemistry patent search
Robert A Stembridge Abstract
1:55 76 Numeric property searching in STN patent databases
Jim Brown Abstract
2:20   Intermission.
2:30 77 Approaches for extraction and “digital chromatography” of chemical data - a perspective from the RSC
David Sharpe, Colin Batchelor, Valery Tkachenko, Kenneth Karapetyan, Antony J Williams, Richard Kidd Abstract
2:55 78 SCRIPDB: A portal for easy access to syntheses, chemicals, and reactions in patents
Abraham Heifets, Igor Jurisica Abstract
3:20 79 CWM Global Search: The internet search engine for chemists and biologists
Guenter Grethe, Hans-Juergen Himmler, Alex Kos Abstract
3:45   Intermission.
3:55 80 Extracting chemical information in a corporate environment with JChem for SharePoint
Tamás Pelcz, Anna Gulyás-Forró Abstract
4:20 81 Federated chemical searching across SharePoint and E-Notebook
Rudy Potenzone, Phil McHale, Megean Schoenberg, Alex Jewett, Kate Blanchard, David Gosalvez, Philip Skinner Abstract
4:45   Concluding Remarks.

MONDAY EVENING

Pennsylvania Convention Center
Hall D

Sci-Mix
R. Bienstock, Organizer
8:00 - 10:00 pm
  2 See previous listing
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  70 See previous listing
  81 See previous listing
  91 WITHDRAWN
  102 See later listing
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  145 See later listing

TUESDAY MORNING

Philadelphia Marriott Downtown
Room 302/303

Herman Skolnik Award Symposium
Henry Rzepa, Peter Murray-Rust, Organizers, Presiding
8:30   Introductory Remarks.
8:35 82 Changing ways of sharing research in chemistry
Henry S Rzepa Abstract
8:55 83 Making the connection between molecular structure and spectroscopy: Jmol, JSpecView, and JCAMP-MOL
Robert M Hanson, Robert Lancashire Abstract
9:10 84 HTML5 enables new methods of distrubuting scientific information
Josef J Polak, Kevin J Theisen Abstract
9:25 85 Chem4Word: Semantic chemical authoring within Microsoft Word
Alex D Wade, Anthony J. G. Hey Abstract
9:40 86 From Smart Tea to blog3: A story of users, laboratories, and the semantic web
Jeremy G Frey Abstract
9:55 87 Blogs and chemical communication
Steven M Bachrach Abstract
10:10   Intermission.
10:20 88 Semantic pipelines to molecular properties
Egon Willighagen Abstract
10:35 89 Using Semantic Web tools to improve chemical collaboration
Omer Casher, Henry Rzepa Abstract
10:50 90 Towards publishing semantic descriptions of Electronic Laboratory Notebook records
Simon Coles, Richard Whitby, Jeremy Frey, Colin Bell, Aileen Day Abstract
11:05 91 WITHDRAWN
11:20 92 Open Source cocktail: Benefits of integrating Cheminformatics and statistical software
Rajarshi Guha Abstract
11:35 93 Avogadro, open chemistry, and chemical semantics
Marcus D Hanwell, Kyle Lutz Abstract

TUESDAY AFTERNOON

Philadelphia Marriott Downtown
Salon H

Herman Skolnik Award Symposium
Henry Rzepa, Peter Murray-Rust, Organizers, Presiding
1:30

94

Can we build artificially intelligent chemists?
Peter Murray-Rust Abstract
1:50 95 Enriching the NWChem computational chemistry software with Chemical Markup Language semantics
Wibe A de Jong, William A Shelton Abstract
2:05 96 Data-rich chemistry inside Wikipedia and other wikis
Martin A Walker Abstract
2:20 97 Progress and directions towards semantic NMR data
Karl T. Mueller, Nancy M. Washton, Nico Adams Abstract
2:35   Intermission.
2:45 98 Natural language parsing for semantic science
Lezan Hawizy, Daniel Lowe, Hannah Barjat, David Jessop, Peter Murray-Rust Abstract
3:00 99 Language, semantics, and chemistry: Why computers need to say what we mean
Robert C Glen Abstract
3:15 100 Automated molecular data extraction using Open Babel and ChemSpotlight: The Semantic Web and Semantic Desktop
Geoffrey R Hutchison Abstract
3:30 101 Crystallographic publishing in the semantic age
Brian McMahon Abstract
3:45 102 Towards semantic materials informatics: Making materials data accessible and useful
Nico Adams, Murray Jensen Abstract
4:00   Intermission.
4:10 103 Exploring large chemical data sets: Interactive analysis and visualization
Kyle Lutz, Marcus D Hanwell Abstract
4:25 104 Chemical classification for the Semantic Web
Janna Hastings, Paula de Matos, Venkatesh Muthukrishnan, Marcus Ennis, Adriano Dekker, Steve Turner, Gareth Owen, Christoph Steinbeck Abstract
4:40 105 Use of InChI on the Internet
Stephen Heller Abstract
4:55 106 ChemSpider compound database as one of the pillars of a semantic web for chemistry
Valery Tkachenko, Antony J Williams, Alexey Pshenichnov, Kenneth Karapetyan, Colin Batchelor, Jonathan Steele, Aileen Day, David Sharpe Abstract
5:10   Award Presentation.

WEDNESDAY MORNING

Philadelphia Marriott Downtown
Room 302/303

Global Opportunities in Chemical Information Cosponsored by PROF, SCHB
Jignesh bhate, Tom Blackadar, Organizers
Rachelle Bienstock, Presiding
9:00   Introductory Remarks.
9:10 107 Translating IUPAC-like chemical nomenclature to and from simplified Chinese
Roger A Sayle, Daniel M Lowe Abstract
9:35 108 Challenges and rewards of starting a small global chemistry business in China
Thomas A Blackadar Abstract
10:00 109 Multilingual WorldWideScience.org
Brian Hitson Abstract
10:25   Intermission.
10:35 110 India - the drunken man's stupor: Eventually we reach...
Jignesh Bhate Abstract
11:00 111 Challenges in sourcing and processing patent information from emerging markets
Andrew McFarlane Abstract
11:25   Moderated Panel Discussion.

 Philadelphia Marriott
Conference Room 307

Chemical Space: Challengers in Visualization and Mining
Jose Medina-Franco, Maciej Haranczyk, Organizers
Maciej Haranczyk, Presiding
8:00   Introductory Remarks.
8:05 112 TorsionAnalyzer: Interactive analysis and exploration of the conformational space
Christin Schärfer, Tanja Schulz-Gasch, Matthias Rarey, Wolfgang Guba Abstract
8:25 113 Knowledge-based characterization of chemistry space and visualization
Barun Bhhatarai, Stephan Schurer Abstract
8:45 114 Definition and visual exploration of the biologically relevant chemical space
Obdulia Rabal, Julen Oyarzabal Abstract
9:05 115 The chemical space mapplet: Interactive access to millions of molecules on your desktop
Jean-Louis Reymond, Mahendra Awale, Lorenz C Blum, Julian Schwartz, Ruud van Deursen Abstract
9:25 116 Quantification of the diversity of chemical libraries: The "Delimited Reference Chemical Subspaces" (DRCS) methodology
Luc Morin-Allory, Vincent Le Guilloux, Lionel Colliandre, Stephane Bourg Abstract
9:45 117 Interactive tools for navigating structure and property space
Lisa Peltason, Daniel Stoffler Abstract
10:05   Intermission.
10:15 118 High-dimensional activity landscape representations
Dagmar Stumpfe, Jürgen Bajorath Abstract
10:35 119 Exploring activity landscapes through molecular reference structures
David Marcus, Hamse Y Mussa, Andreas Bender, Robert C Glen Abstract
10:55 120 Hole filling and library optimization: Application to commercially available fragment libraries
Woody Sherman, Yuling An, Steven L. Dixon Abstract
11:15 121 Visualizing chemical information
Krisztina Boda Abstract
11:35 123 SmallWorld: Efficient maximum common subgraph searching of large databases
Roger A Sayle, Jose C Batista, Andrew Grant Abstract
11:55 122 Evaluation of data quality in currently available compound libraries
Ferenc Szalai, Márk Sándor, Gáspár Körtesi, Enikő Dorogi, Zoltán Szalai, Róbert Kiss Abstract

WEDNESDAY AFTERNOON

Philadelphia Marriott Downtown
Room 302/303

Cheminformatics Opportunities in Personalized Medicine and Chemogenomics
Christoph Steinbeck, David Wild, Organizers, Presiding
1:00   Introductory Remarks.
1:05 124 What works well together? Predicting synergistic combinations
Rajarshi Guha, Lesley Mathews, Don Liu, Paul Shinn, Marc Ferrer, Craig Thomas Abstract
1:25 125 Data-mining of pharmacogenetic data to predict and improve drug safety
John P Overington Abstract
1:45   Intermission.
2:00 126 Chemogenomic approach for QSAR modeling of inhibition activity against five major cytochrome P450 isoforms
Sergii Novotarskyi, Igor V. Tetko Abstract
2:20 127 Activity landscape modeling of PPAR ligands with dual-activity difference maps
Oscar Méndez-Lucio, Jaime Pérez-Villanueva, Rafael Castillo, José L Medina-Franco Abstract
2:40 128 Combining HTS in vitro assays with in silico descriptors for liver toxicity modeling
Ahmed M Abdelaziz, Igor V Tetko Abstract

 Philadelphia Marriott
Conference Room 307

Informatics Approaches to Materials Design
Maciej Haranczyk, Ian Bruno, Organizers
Ian Bruno, Maciej Haranczyk, Presiding
1:30   Introductory remarks.
1:35 129 Data mining and crystal structure informatics in pharmaceutical drug development
Magali Hickey, Peter Wood, Mark Oliveira, Heather Clarke, Michael Zaworotko, Orn Almarsson Abstract
2:00 130 Elaboration of weak intermolecular forces involving terminal alkynes
Eric Bosch Abstract
2:25 131 Role of CSD-derived structural informatics approaches in solid form design strategy
Neil Feeder, Peter T A Galek, Elna Pidcock, Peter A Wood Abstract
2:50   Intermission.
3:05 132 Informatics method to bridge gap between experimental results and simulation for carbon nanotube reinforced composites
Daniel Calto, Atyab Tahir Abstract
3:30 133 Creating a chemical informatics approach to accelerating materials simulations
Michael P. Krein, Gregory S. Ho, Jason J. Poleski, Richard R. Barto Abstract
3:55 134 Descriptors and search tools for porous materials
Richard L Martin, Maciej Haranczyk Abstract
4:20 135 Multicomponent organic solar cells: High performance multi-objective searches
Geoffrey R Hutchison Abstract

THURSDAY MORNING

Philadelphia Marriott
Franklin Hall 6

General Papers Chemical Databases, Drug Discovery, and Chemical Structure Representation
Rachelle Bienstock, Organizer, Presiding
8:30 136 Relative drug likelihood: Going beyond "drug-likeness"
Matthew M Segall Abstract
8:50 137 Statistical significance of 3D molecular similarity scores
Sunghwan Kim, Evan E Bolton, Stephen H Bryant Abstract
9:10   Intermission.
9:15 138 Delivering an online service for validating and standardizing chemical structure files using the ChemSpider platform
David Sharpe, Antony Williams, Valery Tkachenko, Colin Batchelor, Kenneth Karapetyan Abstract
9:35 139 How can the International Chemical Identifier (InChI) be extended to non-trivial chemicals?
Valery Tkachenko, Antony J Williams, Yulia Borodina, Frank Switzer, Tyler Peryea, Larry Callahan Abstract
9:55 140 Serving up and consuming community content for chemists using wikis
Antony J Williams, Alexey Pshenichnov, Valery Tkachenko, Aileen Day, Sean Ekins Abstract
10:15   Intermission.
10:20 141 Use of an institutional repository to promote chemical sciences collections at the University of Florida
Donna T. Wrublewski, Lois J. Widmer, Laurie N. Taylor, Dina Benson Abstract
10:40 142 Linked data and the globally harmonized health and safety (GHS) system
Jeremy G Frey, Mark I Borkum, Simon J Coles Abstract

THURSDAY AFTERNOON

Philadelphia Marriott
Franklin Hall 6

Legal, Patent, and Digital Rights Management in Publishing Cosponsored by PROF
Judith Currano, Charles Huber, Organizers
Judith Currano, Presiding
1:00   Introductory Remarks.
1:10 143 How to find references that inherently anticipate pharmaceutical patents
David Gange Abstract
1:30 144 Digital rights drain? Implications for library services
Leah Solla Abstract
1:50 145 Digital rights management and e-books: Perspectives from a research library
Tara Cataldo, Donna T. Wrublewski Abstract
2:10 146 Right to retain: The problems of preserving digital content
Ian Bogus, Judith N. Currano Abstract
2:30 147 Finding an alternative to restrictive digital rights mangement: The Momentum Press approach
David Parker Abstract
2:50   Roundtable Discussion.
3:50   Concluding Remarks.

 

COMP Symposia
Cosponsored by CINF

Emilio Esposito, Scott Wildman, Program Chairs

SUNDAY MORNING

Pennsylvania Convention Center
Room 118 B

Computational Approaches to Spectroscopy Analysis Cosponsored by ANYL, BIOL, CINF, PHYS
Emilio Esposito, Organizer
Hai Nguyen, Presiding
8:30 36 Unraveling the mechanisms of O2 activation by size-selected gold nanoclusters: A combined photoelectron spectroscopic and density functional approach
Rhitankar Pal
9:00 37 Progress in the use of non-negative matrix factorization, clustering, and covariance techniques in the analysis of complex reaction mixtures via NMR
David A. Snyder.
9:30 38 Estimating NMR parameters and the nature of ionic atmosphere of nucleic acids from simulation
George M Giambasu, Tyler Luchko, Darrin M York, David A Case
10:00   Intermission.
10:15 39 Thermodynamics of prediction
Susanne Still, David A Sivak, Anthony J Bell, Gavin E Crooks
10:45 40 From spectroscopic properties to high accuracy protein active site structures: A quantum chemical pathway
Yong Zhang
11:15 41 Identifying relativistic effects on (hyper)polarizabilities
Adam C Chamberlin, Radovan Bast, Kenneth Ruud

Pennsylvania Convention Center
Room 115 C

Computational Approaches to Spectroscopy Analysis Cosponsored by ANYL, BIOL, CINF, PHYS
Emilio Esposito, Organizer
Hai Nguyen, Presiding
9:00 13 Prediction of Raman spectrum of high-pressure phases of complex organic crystals using a combined periodic DFT-D/ONIOM approach
Sammer M. Tekarli, Santanu Chaudhuri
9:30 14 Computational modeling of optical properties of lanthanide ions doped hexagon (β) - NaYF4 nanocrystals for laser spectroscopy
Ge Yao, Mary T Berry, Stanley May, Dmitri S Kilin.
10:00   Intermission.
10:15 15 Electronic and magnetic properties of a tris(hydroxo)-bridged chromium dimer, a challenge for DFT
Simon J Bennie, Joseph J.W. McDouall, David Collison
10:45 16 p-n Doped silicon quantum dot
Jiangchao Chen, Andrew Schmitz, Dmitri Kilin
11:15 17 Anisotropy of exciton localizations in silicon nanowires
Dmitri Kilin, Sergei Tretiak

Pennsylvania Convention Center
Room 115 A

CSAR 2011-2012 Benchmark Exercise Cosponsored by BIOL, CINF, MEDI, PHYS
Heather Carlson, James Dunbar, Organizers
Heather Carlson, Presiding
9:00   Introductory Remarks.
9:10 1 Community structure-activity resource (CSAR) benchmark exercise 2011: Genesis of the datasets and selection of a blinded congeneric series for the exercise
James B. Dunbar Jr., Jeanne A Stuckey, Richard D Smith, Emilio Xavier Esposito, Heather A Carlson
9:45 2 Community structure-activity resource (CSAR) benchmark exercise 2011: Docking and relative ranking of a blinded congeneric series of compounds
Kelly L. Damm-Ganamet, Jeanne A. Stuckey, Richard D. Smith, James B. Dunbar Jr, Heather A. Carlson.
10:20   Intermission.
10:35 3 WITHDRAWN
11:10 4 Predicting relative binding affinities of congeneric series of ligands: A prospective docking study using Prime docking
Chakrapani Kalyanaraman, Matthew P Jacobson
11:45 5 Exercise on 2011 CSAR Benchmark using the iterative knowledge-based scoring functions ITScore and STScore of the MDock software: What we have learned
Sheng-You Huang, Sam Z Grinter, Chengfei Yan, Lin Jiang, Xiaoqin Zou

Pennsylvania Convention Center
Room 117

Drug Discovery - Ligand-based Cosponsored by BIOL, CINF, MEDI
Scott Wildman, Y. Jane Tseng, Organizers
Y. Jane Tseng, Presiding
8:30 29 Kernel partial least squares (KPLS) applications to understanding SAR and improving confidence in predictions
Woody Sherman, Yuling An, Steven L. Dixon
9:00 30 Estimating prediction confidence in QSAR
David J Wood, Lars A Carlsson, Martin Eklund, Jonna C Stålring.
9:30 31 Reducing the bias in ligand-based modelling
Nigel Duffy, Brad Dolin, Yuanjian Feng, Jessen Yu.
10:00   Intermission.
10:15 32 Dynamic SA/reports: Analyzing current project and HTS data by interactive selection of frequently-occurring scaffolds
Deepak Bandyopadhyay.
10:45 33 Novel, comprehensive pharmacophore hypotheses for anthrax toxin lethal factor (LF) inhibitors
Elizabeth A Amin, Ting-Lan Chiu
11:15 34 Identification of novel fungal histone acetyltransferase Rtt109 inhibitors using in vitro HTS, pharmacophore mapping, 3D-QSAR, shape-based searching, and SVM
Xia Zhang, Jonathan C Solberg, Derek J Hook, Michael A Walters, Elizabeth A Amin
11:45 35 Development of HIV inhibitors targeting cyclophilin A guided by free energy perturbation calculations
Orlando Acevedo

Pennsylvania Convention Center
Room 118 B

Material Science Cosponsored by CINF, COLL, INOR, ORGN, PHYS, PMSE, POLY, TOXI
Maciej Haranczyk, Organizer
9:00   Introductory Remarks.
9:05 42 Reactive molecular dynamics simulation on the disintegration of kapton and silicon-oxygen compound in kapton-poss during oxygen bombardment
Ali Rahnamoun, Adri van Duin
9:35 43 Study of embrittlement induced by sulfur segregation on metal grain boundary using the ReaxFF force field
Yun Kyung Shin, Adri van Duin, Shaun Kwak, Alex Vasenkov.
10:05 44 ReaxFF based molecular dynamics simulation of Fullerene self assembly and decomposition of hot Fullerene and onion like carbon allotropes
Sriram Goverapet Srinivasan, Adri C T van Duin.
10:35   Intermission.
10:50 45 General systematic property optimization in chemical space
Berend Christopher Rinderspacher
11:20 46 Molecular structure of P3HT/PCBM polymer blend nanoparticles
Angela Crotty, Iffat H Nayyar, Artem E Masunov, Zhiang Hu, Andre J Gesquiere

Pennsylvania Convention Center
Room 115 B

Membranes Cosponsored by BIOL, CINF, COLL, MEDI, PHYS
Michael Feig, Organizer
Brian Fochtman, Presiding
8:30 6 Elucidating the structure of hydrogen ion channel of Ciona intestinalis
Adam C Chamberlin, Sergei Noskov
9:00 7 Free energetics of polyarginine permeation into model lipid bilayers
Yuan Hu, Sandeep Patel.
9:30 8 Watching ions and water conduction through sodium channels
Werner Treptow, Leticia Stock, Vincenzo Carnevale, Michael Klein.
10:00 9 Molecular dynamics simulations of ion binding and protonation of phosphatidylinositol bisphosphate (PIP2)
David R Slochower, Peter J Huwe, Ryan P Bradley, Ravi Radhakrishnan, Paul A Janmey.
10:30   Intermission.
10:45 10 WITHDRAWN.
11:15 11 Domain registration in membranes: Evidence from coarse grained molecular dyamincs
Preston Moore, Diego Pantano
11:45 12 Mesoscale simulations of curvature inducing proteins partitioning along mean curvature gradients
Richard Tourdot, Ramakrishnan Natesan, Ravi Radhakrishnan

Pennsylvania Convention Center
Room 116

Molecular Mechanics - Proteins: We Like to Think of Proteins as 'Smart Polymers' Cosponsored by BIOL, CINF, MEDI, PHYS
Michael Feig, Organizer
Luke Achenie, Presiding
9:00 24 Predicting the agonist-bound structures of the glucagon-like peptide 1 receptor, a class B G protein-coupled receptor
Andrea Kirkpatrick, Jiyoung Heo, Ravinder Abrol, William A Goddard
9:30 25 Molecular recognition and epigenetic modulation: The LSD1-CoREST nanoscale clamp prototype system
Nadeem Ahmad Vellore, Riccardo Baron
10:00 26 Efficient explicit-solvent simulations of barnase-barstar binding events
Matthew C Zwier, Lillian T Chong.
10:30   Intermission.
10:45 27 Blind prediction in the SAMPL3 challenge: Transfer energies, host-guest binding affinity, and fragment binding affinity
Matthew T Geballe, Anthony Nicholls, A Geoffrey Skillman
11:15 28 Molecular dynamics analysis of the binding affinities of seven ligands of human epidermal growth factor receptor
Jeffrey M. Sanders, Matthew E. Wampole, Mathew L, Thakur, Eric Wickstrom

SUNDAY AFTERNOON

Pennsylvania Convention Center
Room 115 A

CSAR 2011-2012 Benchmark Exercise Cosponsored by BIOL, CINF, MEDI, PHYS
Heather Carlson, James Dunbar, Organizers
Heather Carlson, Presiding
2:00 47 Ligand interaction scoring algorithm (LISA) and CSAR
Kenneth M. Merz, Zheng Zheng
2:35 48 Application of the docking program SOL for CSAR benchmark
Alexey V. Sulimov, Danil K. Kutov, Ekaterina V Katkova, Vladimir B Sulimov
3:10 49 SPA: A novel scoring function for protein-ligand binding
Zhiqiang Yan, Jin Wang.
3:45   Intermission.
4:00 50 MedusaDock: A rapid flexible docking approach
Feng Ding, Nikolay V Dokholyan
4:35 51 Predicting poses and binding affinity of CSAR ligands using structure based and ligand based approaches
Denis Fourches, Eugene Muratov, Feng Ding, Ashutosh Tripathy, Nikolay Dokholyan, Alexander Tropsha
5:10 52 Results for FRED on the CSAR data set
Gregory L Warren, Mark McGann, Paul Hawkins

Pennsylvania Convention Center
Room 117

Drug Discovery - ADME-toxicology Cosponsored by BIOL, CINF, MEDI, TOXI
Y. Jane Tseng, Scott Wildman, Organizers
Edward Sherer, Presiding
1:30 77 Quantitatively interpreted enhanced inhibition of cytochrome P450s by heteroaromatic rings containing nitrogen
Nathan J Kidley, Andrew G Leach
2:00 78 Computational method for the prediction of P450-mediated metabolism: Development, validation, and significance
Nicolas Moitessier
2:30 79 QSAR modeling for the evaluation of aryl hydrocarbon receptor activators
Ahmed Abdelaziz, Alexander Safanyaev, Vladimir A Palyulin, Igor V Tetko.
3:00   Intermission.
3:15 80 Structure-based model for predicting serum albumin binding
Katrina W Lexa, Matthew P Jacobson
3:45 81 QSAR modeling of human liver microsomal stability
Alexey V Zakharov, Megan L Peach, Markus Sitzmann, Igor V Filippov, Marc C Nicklaus
4:15 82 ToxAlerts: Online database of toxicological structure alerts
Iurii Sushko, Elena Salmina, Vladimir Potemkin, Igor V Tetko

Pennsylvania Convention Center
Room 118 B

Material Science Cosponsored by CINF, COLL, INOR, ORGN, PHYS, PMSE, POLY, TOXI
Maciej Haranczyk, Organizer
Seonah Kim, Presiding
1:30 90 Density functional investigation of HAP dissolution and the influence of organic materials
Manuel Vega-Arroyo, Gena Tribble, Rolf Arvidson, Andreas Luttge, S. Ray Taylor
2:00 91 Pancake bonds: Unusually short van der Waals contacts or very long multicenter covalent bonding in SN and SeN containing dimers of radicals
Miklos Kertesz, Habtamu Z. Beneberu, Yonghui Tian
2:30 92 Calculations of electronic relaxation times in semiconductor nanocrystals
Alex Kutana, Dmitri S Kilin
3:00   Intermission.
3:15 93 MD simulation of Al grain mixing/diffusion in Fe/Ni matrices
Osvalds Verners, Adri C.T. van Duin, Yun Kyung Shin.
3:45 94 Preferable binding of polystyrene sulfonate on calcite surfaces
Jia-Wei Shen, Chunli Li, Nico F.A. van der Vegt, Christine Peter
4:15 95 Computational perspective on the relationship between structure and optical properties of polypyrene materials
Martijn Zwijnenburg

Pennsylvania Convention Center
Room 116

Molecular Mechanics - Proteins Cosponsored by BIOL, CINF, MEDI, PHYS
Michael Feig, Organizer
Emilio Esposito, Presiding
1:30 73 Computational study of the possible coupling between subunits of the enzyme glutamine-dependent amidotransferase (GatCAB)
Liangjun Zhao, Sajeewa W Dewage, Michael J Bell, Keng-Ming Chang, Shirin Fatma, Nilesh Joshi, Gayathri Silva, Andres Cisneros, Tamara L Hendrickson
2:00 74 Computational structural elucidation of benzylsuccinate synthase: A bridge to understanding free-radical chemistry in the anaerobic biodegradation of hydrocarbons
Vivek S. Bharadwaj, C. Mark Maupin, Anthony M. Dean
2:30 75 Allostery in nuclear receptor proteins: Molecular mechanisms from molecular dynamics simulations
Roland H Stote, Yassmine Chebaro, Ismail Amal, Annick Dejaegere
3:00   Intermission.
3:15 76 Enzyme simulation of the MOVB method
Jaebeom Han, Alessandro Cembran, Jiali Gao.

MONDAY MORNING

Pennsylvania Convention Center
Room 115 A

Computational Study of Water Cosponsored by BIOL, CINF, MEDI, PHYS
Emilio Esposito, Organizer
8:30 96 Hydrogen bond dynamics and vibrational spectroscopy of aqueous system: An ab initio molecular dynamics study
Anwesa Karmakar
9:00 97 Ab initio molecular dynamics study of dissociation of water under an electric field
Antonino Marco Saitta, Franz Saija, Paolo V Giaquinta
9:30   Intermission.
9:45 98 Chemistry in water with adaptive QM/MM simulations
Rosa Bulo, Carine Michel, Paul Fleurat-Lessard, Philippe Sautet, Lucas Visscher
10:15 99 Soft-sticky dipole-quadrupole-octopole model of liquid water
Mingliang Tan, Toshiko Ichiye
10:45 100 Benchmark structures and binding energies of small water clusters
George C. Shields, Berhane Temelso
11:15 101 Effect of van der Waals interactions on the structure of liquid water
Robert A. DiStasio Jr., Zhaofeng Li, Roberto Car

Pennsylvania Convention Center
Room 117

Drug Discovery - Methodology: Got Methodologies? We do! Cosponsored by BIOL, CINF, MEDI
Scott Wildman, Y. Jane Tseng, Organizers
8:30 128 Structure-based lead optimization: Force-field-based minimizations in the blink of an eye
Lennart Heinzerling, Robert Klein, Matthias Rarey
9:00 129 Unraveling the binding of histidine kinase inhibitors by molecular dynamics simulations
Mercedes Alfonso-Prieto, Sharon M. Loverde, Michael L. Klein
9:30 130 Use of single step free energy perturbation to estimate relative binding affinity by fragment modification
E. Prabhu Raman, Kenno Vanommeslaeghe, Alexander D MacKerell
10:00 131 Identifying drug binding locations and poses using Hamiltonian replica exchange molecular dynamics
Kai Wang, John D. Chodera, Michael R. Shirts
10:30   Intermission.
10:45 132 Prediction of protein-protein binding free energies
Thom Vreven, Howook Hwang, Brian G Pierce, Zhiping Weng.
11:15 133 How to pick a winning team: Assessment of computationally derived protein ensembles in protein-ligand docking
Barbara Sander, Oliver Korb, Jason C. Cole, Jonathan W. Essex.
11:45 134 Development of a de novo design platform for DOCK: Application to HIV gp41
William J. Allen, Robert C. Rizzo

Pennsylvania Convention Center
Room 116

Molecular Mechanics - Methodologies Cosponsored by BIOL, CINF, MEDI, PHYS
Michael Feig, Organizers
Dong Fang, Presiding
8:30 121 Accurate and efficient treatment of many-body van der Waals interactions with applications in biology, chemistry, and physics
Robert A. DiStasio Jr., Alexandre Tkatchenko
9:00 122 Recursive Taylor series expansion method for rigid body molecular dynamics
Alexey V Akimov
9:30 123 Evaluating the grand-canonical partition function of atomic and molecular fluids using expanded Wang-Landau simulations
Caroline Desgranges, Jerome Delhommelle
10:00 124 Using simulation of simulations to evaluate and improve Reservoir Replica Exchange methods through transition state theory
Asim Okur, Daniel Smith, Bernard R Brooks.
10:30   Intermission.
10:45 125 Simple tests for validity when sampling thermodynamic ensembles
Michael R. Shirts.
11:15 126 Validation of free energy calculation methods: Thermodynamic sampling of large parameter spaces using multistate reweighting methods
Michael R. Shirts, Himanshu Paliwal.
11:45 127 Thermodynamic metrics and optimal paths
David A Sivak, Gavin E Crooks

Pennsylvania Convention Center
Room 118 B

Scripting and Programming: Drug Discovery and High-Performance Computing in the Cloud Cosponsored by BIOL, CINF, MEDI
Brian Moldover, Zheng Yang, Organizers
Sajeewa Walimuni Dewage, Presiding
8:30   Introductory Remarks.
8:35 141 Cloud computing platform for high-throughput virtual screening and drug discovery
Samuel Wein
9:05 142 Integrative approach to drug discovery: Targets, compounds, and econometrics in the cloud
Gerald Wyckoff
9:35 143 Development of the CHARMM interface and graphics WEB portal as a platform for computer aided drug design
Yuri Pevzner, Henry L Woodcock
10:05   Intermission.
10:20 144 Scaling drug discovery pipelines at mcule.com
Ferenc Szalai, Márk Sándor, Gáspár Körtesi, Zoltán Szalai, Enikő Dorogi, Róbert Kiss
10:50 145 Numatix: Cloud compute for computational chemistry
Nigel Duffy, Brandon Allgood, Brad Dolin, Sean Sylvis, Simon Wilkinson, Jessen Yu.
11:20 146 Novel uses of CHARMM for highly distributed and cloud resources: MSCALE and CHARMMing
Benjamin Miller, Henry Lee Woodcock, Bernard Brooks.
11:50   Concluding Remarks.

MONDAY AFTERNOON

Pennsylvania Convention Center
Room 115 A

Computational Study of Water Cosponsored by BIOL, CINF, MEDI, PHYS
Emilio Esposito, Organizer
1:30 147 Recent advances in the WaterMap methodology: Applications to druggability, binding energy prediction, and drug discovery
Woody Sherman, Robert Abel, Goran Krilov, Thijs Beuming, Ramy Farid
2:00 148 Role of water in ubiquinol binding in the electron transfer protein complex cytochrome bc1
Ralph A. Wheeler, Bao-Linh Nguyen.
2:30 149 Simulation of water in protein interior
Igor Leontyev, Alexei Stuchebrukhov.
3:00 150 Predicting water molecule positions in biomolecules from 3D-RISM density: Applications to low resolution X-ray and homology models
Jean-François Truchon, Paul Labute
3:30   Intermission.
3:45 151 Insights into solvation of DNA from molecular dynamics and 3D-RISM
Tyler Luchko, George M. Giambasu, Darrin M. York, David A. Case
4:15 152 Water transport through carbon nanotubes with modified water models
Minseok Song, Mark A. Snyder, Jeetain Mittal
4:45 153 Role of water structure in various influenza neuraminidase species in complex with common inhibitors
Daniel J Sindhikara, Jiraporn Tengrang, Thanyada Rungrotmongkol, Fumio Hirata

Pennsylvania Convention Center
Room 117

Drug Discovery - Methodology Cosponsored by BIOL, CINF, MEDI
Scott Wildman, Y. Jane Tseng, Organizers
Thuy Hien Nguyen, Presiding
1:30 180 Less is more: Visualizing protein-ligand complexes in 2D
Christian Lemmen
2:00 181 Exploring the development of fragment hits into leads using the protein mapping program FTMap
Dima Kozakov, David R Hall, Ci Ho Ngan, Brandon S Zerbe, Sandor Vajda
2:30 182 Fuzzy pharmacophore feature pairs
Paul J Kowalczyk.
3:00 183 Converging methodologies: Where data alchemy meets data application
Emilio Xavier Esposito
3:30   Intermission.
3:45 184 False discovery rate: A “New Deal” for shape searching?
Paul C Hawkins, Tom Darden, Anthony Nicholls
4:15 185 Analytical expression for the hit-rate
Nigel Duffy
4:45 186 Length and time scales of coarse-grain molecular dynamics simulations: A detailed review
Kenny Nguyen, Preston B Moore
5:15 187 Advances in the treatment of explicit solvent for understanding SAR and computing binding energies
Woody Sherman, Robert Abel, Thijs Beuming, Goran Krilov, Ramy Farid

Pennsylvania Convention Center
Room 118 B

Drug Discovery in Tyrosine Kinase Inhibitors and Drug Resistance Cosponsored by BIOL, CINF, MEDI
Haizhen Zhong, Joel Bowen, Organizers
1:30   Introductory Remarks.
1:35 192 Understanding kinase activation of ALK in neuroblastoma patients
Peter Huwe, Ravi Radhakrishnan
2:05 193 Tyrosine kinase inhibition: Ligand binding and conformational change in c-Kit and c-Abl
Eamonn F Healy, Peter J. King
2:35 194 Approaches to the design of protein-protein interaction blockers targeting VEGF receptor signaling
Ethan W. Taylor, Kalyan Paila.
3:05 195 Solenopsin A derivatives: Design, synthesis, and biological evaluations
J. Phillip Bowen, Shavon Ford, Michael Baker, Jack Arbiser.
3:35   Intermission.
3:50 196 Confine-and-release thermodynamic integration reveals components of PKG regulatory domain specificity
Paul M Gasper, J. Andrew McCammon
4:20 197 Design, synthesis, and docking studies of phosphatidylinositol 3-kinase alpha inhibitors
Haizhen Zhong, Dima A Sabbah, Neka A Simms, Michael G Brattain, Jonathan L Vennerstrom
4:50 198 Cheminformatic studies of human Eph receptorome
Xiang S Wang
5:20   Concluding Remarks

Pennsylvania Convention Center
Room 116

Molecular Mechanics - Force Fields, Cosponsored by BIOL, CINF, MEDI, PHYS
Michael Feigen, Organizer
Nadeem Vellore, Presiding
1:30 174 Developing a high-quality scoring function for membrane protein structures based on specific inter-residue interactions
Andrew J Heim, Zhijun Li.
2:00 175 Computational design of peptide nucleic acid conjugates for imaging oncogenic KRAS2 mRNA in vivo
Matthew E. Wampole, Jeffrey M. Sanders, Mathew L. Thakur, Eric Wickstrom.
2:30 176 Development of OPLS-AA force field parameters for QM/MM ionic liquid simulations
Orlando Acevedo, Caley Allen, Billy W McCann, Somisetti V Sambasivarao
3:00   Intermission.
3:15 177 Automatic and unbiased self-training method for updating a reactive force field using QM calculations
Michael R. Salazar
3:45 178 Transferable all-atom force field for hydrofluorocarbons
Samuel J Keasler, Nathan E Schultz, Richard B Ross, J. Ilja Siepmann.
4:15 179 Anisotropy of van der Waals atomic radii of selected main group elements
Miklos Kertesz, Hamed Eramiang

Pennsylvania Convention Center
Room 118 A

Simulations of Crowding, Confinement, and Cellular Environments Cosponsored by BIOL, CELL, CINF, COLL, MEDI, PHYS
Michael Feig, Organizer
1:30 188 On the importance of hydrodynamic interactions in lipid membrane formation
Jeffrey Skolnick, Tadashi Ando.
2:10 189 Factors influencing the diffusion and association of molecules explored with Brownian dynamics
Maciej Długosz, Jan M Antosiewicz, Paweł Zieliński, Joanna Trylska.
2:50 190 Interplay between molecular scale hydrodynamics and the free energy surface in nanoparticle hydrophobic assembly
Joseph A Morrone, Jingyuan Li, Bruce J Berne
3:30   Intermission.
3:45 191 Macromolecular crowding and anomalous diffusion: Causes and consequences
Matthias Weiss

TUESDAY MORNING

Pennsylvania Convention Center
Room 118 B

Characterization and Screening of Databases of Porous Materials Cosponsored by CINF, ENFL, INOR, PHYS, PMSE, POLY
Michael Deem, Maciej Haranczyk, Organizers
8:30   Introductory Remarks.
8:35 242 Screening hypothetical porous organic molecules
Kim E Jelfs, Andrew I Cooperkar
9:05 243 3D characterization of microporous networks
Eric L. First, Chrysanthos E. Gounaris, James Wei, Christodoulos A. Floudas
9:35 244 High-throughput generation and screening of metal-organic frameworks for adsorption applications
Christopher E Wilmer, Benjamin J Sikora, Yamil J Colon, Ki Chul Kim, David Fairen-Jimenez, Michael L Greenfield, Randall Q Snurr
10:05   Intermission.
10:20 245 Finding low-energy porous polymorphs for compounds traditionally considered dense
Martijn A Zwijnenburg, Stefan T Bromley.
10:50 246 Informatics tools for analysis of porous materials
Maciej Haranczyk, Richard Luis Martin, Chris Rycroft.
11:20 247 Similarity-driven discovery of porous materials for practical and industrial applications
Maciej Haranczyk, Richard Luis Martin

Pennsylvania Convention Center
Room 117

Drug Discovery - Target-based Cosponsored by BIOL, CINF, MEDI
Scott Wildman, Y. Jane Tseng, Organizers
Thuy Hien Nguyen, Presiding
8:30 229 Analysis of the protein preparation process and implications in virtual screening
Madhavi Sastry, Woody Sherman.
9:00 230 Screening for potent inhibitors to combat resistance
Wei Wang
9:30 231 Structure-based virtual screening considering multiple hydrogen interaction patterns
Angela M Henzler, Sascha Urbaczek, Matthias Rarey
10:00 232 General applicability of HYDE scoring: Applications to protein-protein interactions
Marcus Gastreich, Gudrun Lange, Carsten Detering, Christian Lemmen, Nadine Schneider, Matthias Rarey
10:30   Intermission.
10:45 233 Genetic algorithm guided optimization of pharmacophore models for estrogen receptor agonists
Hongmao Sun, Srilatha Sakamuru, Menghang Xia, Christopher P Austin, Ruili Huang
11:15 234 Designing protein-protein interaction inhibitors of apicomplexan parasites
Sandhya Kortagere, Joanne Morrisey, Thomas Daly, Suchi Goel, James Burns, Lawrence Bergman, Channe Gowda, Akhil Vaidya.
11:45 235 LeadOp: Structure-based fragment hopping for lead optimization using pre-docked fragment database
Yufeng Jane Tseng

Pennsylvania Convention Center
Room 116

Molecular Mechanics - Force Fields Cosponsored by BIOL, CINF, MEDI, PHYS
Michael Feig, Organizer
Eleonora Gianti, Presiding
8:30 223 Conformational propensity of the 20 amino acids from all-atom molecular dynamics simulations of 400 tetrapeptides (GXXG) and its implication on internal parameter optimization for coarse grain model of protein
Zhiwei Liu, Thuy Hien Nguyen, Preston B. Moore.
9:00 224 Conformational behavior of a sulfonamide containing peptide studied using the CHARMM general force field
Wenbo Yu, Xibing He, Kenno Vanommeslaeghe, Alexander D MacKerell
9:30 225 Parameretization of coupled torsional parameters for arylamide foldamers based on the full 2D energy map
Eduardo M Sproviero, Vojislava Torbica-Pophristic
10:00   Intermission.
10:15 226 ParamChem force field parametrization engine: Initial guess generation and dihedral parameter optimization
Kenno Vanommeslaeghe, Ning Shen, Narendra K. Polani, Ye Fan, Jayeeta Ghosh, Chathura Herath, Suresh Marru, Marlon Pierce, Sudhakar V. Pamidighantam, Michael Sheetz, Alexander D MacKerell, Jr.
10:45 227 Ligandbook – an online repository for small and drug-like molecule force field parameters
Jan Domanski, Oliver Beckstein, Bogdan I Iorga.
11:15 228 Force field optimization using binding data: Application to β-cyclodextrin host-guest systems
Lauren Wickstrom, Emilio Gallicchio, Ronald Levy.

TUESDAY AFTERNOON

Pennsylvania Convention Center
Room 116

Molecular Mechanics - Force Fields Cosponsored by BIOL, CINF, MEDI, PHYS
Michael Feig, Organizer
Lingling Jiang, Presiding
1:30 273 MDEC: A new approach to non-polarizable force fields
Igor Leontyev, Alexei Stuchebrukhov
2:00 274 Current status of the CHARMM Classical Drude oscillator polarizable force field for proteins
Pedro E.M. Lopes, Alexander D. MacKerell Jr..
2:30 275 Development of a CHARMM polarizable force field for aldehydes, ketones, acyclic polyalcohols, and acyclic monosaccharides using the Drude oscillator model
Xibing He, Pedro E. M. Lopes, Alexander D. MacKerell
3:00   Intermission.
3:15 276 Applications of a polarizable force field to computing protein pKa values and modeling protein-ion binding
George A. Kaminski
3:45 277 Solvation of amphiphilic molecules by SSDQO water
Mingliang Tan, Joseph R Cendagorta, Toshiko Ichiye.

Pennsylvania Convention Center
Room 118 B

Perspectives in Applied Computational Methods Cosponsored by BIOL, CINF, MEDI
Cynthia Bancale, Raul Alvarez, Carsten Detering, Organizers
1:30   Introductory Remarks.
1:35 291 Computation takes a community
Frank K Brown
2:20   Intermission.
2:40 292 Coevolution of antibody stability and Vκ CDR-L3 canonical structure
Jinquan Luo
3:25   Intermission.
3:45 293 Data-driven docking: When dock'n it old school just doesn't cut it!
Lance M Westerhoff, Oleg Borbulevych, Joshua A Plumley.

Pennsylvania Convention Center
Room 118 A

Simulations of Crowding, Confinement, and Cellular Environments Cosponsored by BIOL, CELL, CINF, COLL, MEDI, PHYS
Michael Feig, Organizer
1:00 284 Crowding effects on protein association
Arun Yethirajov
1:40 285 Effects of macromolecular crowding on protein folding and stability
Douglas Tsao, Nikolay V Dokholyan.
2:20 286 Atomistic simulations of protein folding and binding under crowding
Huan-Xiang Zhou
3:00 287 Protein stability in cellular environments from multiscale simulations
Michael Feigu
3:40   Intermission.
3:55 288 Hydration structure and dynamics under protein crowding environments
Yuji Sugita, Ryuhei Harada, Michael Feig.
4:35 289 Osmophobics and hydrophobics: The changing landscape of protein folding
Monte Pettitt.
5:15 290 Folding of multidomain and conjugated proteins: Intramolecular crowding effects
Yaakov (Koby) Levy

Pennsylvania Convention Center
Room 117

Understanding and Predicting the Role of Water in Drug Design Cosponsored by BIOL, CINF, MEDI, PHYS
Jean-Francois Truchon, Raul Alvarez, Vijay Pande, Organizers
1:30   Introductory Remarks.
1:35 278 Exploiting ordered waters in structure-based inhibitor discovery
Marcus Fischer, Ryan Coleman, Brian K Shoichet
2:05 279 New approach to molecular simulation: Predicting the role of water in protein structure, dynamics, and function
Vijay S Pande
2:35 280 WATMD: Water analysis tools for molecular dynamics
Daniel McKay
3:05   Intermission.
3:20 281 Why is Gleevec a specific and potent inhibitor of Abl but not of c-Src?
Yilin Meng, Yen-Lin Lin, Wei Jiang, Benoit Roux.
3:50 282 Understanding the role of water network stabilisation in rational drug design
Michael S. Bodnarchuk, Russell Viner, Jonathan W. Essex
4:20 283 Molecular dynamics simulation directed rational design of inhibitors targeting drug-resistant mutants of influenza A virus M2
Jun Wang, Chunlong Ma, Giacomo Fiorin, Vincenzo Carnevale, Tuo Wang, Fanghao Hu, Robert A Lamb, Lawrence H Pinto, Mei Hong, Michael L Klein, William F DeGrado.

TUESDAY EVENING

Pennsylvania Convention Center ,
Hall G

Poster Session Cosponsored by BIOL, CINF, COLL, ENFL, GEOC, INOR, MEDI, ORGN, PHYS, PMSE, POLY, TOXI, YCC
Emilio Esposito, Organizer
6:00 - 8:00
  305 Calculation of frequency-dependent second hyperpolarizabilities for solution-phase organic molecules: Density functional theory approach
Shih-I Lu
  306 Scalable quantum chemical approaches for the study of protected gold nano-clusters
Sandipan Banerjee, John A Montgomery, Jose A Gascon
  307 First-principles calculations for NaTaO3 surfaces
Xiang Liu, Karl Sohlberg
  308 Understanding the helical wrapping of poly(phenylene-ethynylene) polymers about single-walled carbon nanotubes using molecular simulations
Christopher D. Von Bargen, Christopher M. MacDermaid, Colleen S. Murrett, One-Sun Lee, Michael J. Therien, Jeffery G. Saven
  309 Investigations of the impact of ribosomal modification on the binding of the antibiotic telithromycin using Grand-Canonical Monte Carlo and molecular dynamics simulations
Meagan C Small, Rodrigo B Andrade, Alexander D MacKerell, Jr.
  310 Modeling and virtual screening of the D2 dopamine receptor
Xin Hu, Noel Southall, Elena Barnaeva, Melanie Bryant-Genevier, Steve Titus, Jingbo Xiao, Marc Ferrer, Juan Marugan, R. Benjamin Free, David R. Sibley.
  311 (Ala)4-X-(Ala)4 as a model system for the optimization of the χ1 and χ2 amino acid side chain dihedral empirical force field parameters
Jihyun Shim, Xiao Zhu, Robert B. Best, Alexander D. MacKerell Jr.
  312 Quantum mechanical/molecular mechanical simulations: An efficient strategy to calculate vibrational Stark shift
Sirish K Lakkaraju, Ashley R McDonald, Alexander D MacKerell
  313 Targeting the alternative gene splicing related proteins: Identification of potent and selective cdc2-like (Clk) kinase inhibitors
Min Shen, Andrew S. Rosenthal, Bryan T. Mott, Cordelle Tanega, Douglas S. Auld, Christopher P. Austin, David J. Maloney, Craig J. Thomas.
  314 Charge dependent behavior of substrate arginine in the arginase I environment
Shanthi Nagarajan, Fengtian Xue, Alexander D. MacKerell Jr.
  315 Optimization of the CHARMM Drude polarizable force field for DNA
Alexey Savelyev, Chris Baker, Alexander Mackerell.
  316 Dynamics of heavy water inside the solvation shell of iodide ion: A first principle molecular dynamics study
Anwesa Karmakar
  317 Developing first-order continuum Fuzzy-Border solvation model and applying for calculating pKa values of substituted phenols and hydration energies of small molecules
Ity Sharma, George A Kaminski
  318 MD simulation studies to explore the behavior of peptide-based hydrogels
Muhammad S Noon, Alexander D MacKerell, Jr.
  319 Solvent effects on vibrational peak of carbonyl group in substituted Urea derivatives: ONIOM-PCM study
Pansy D Patel, Kenneth B Wiberg, Giovanni Scalmani, Michael J Frisch.
  320 Conformational properties of (1→6)-linked oligosaccharides
Dhilon S Patel, Robert Pendrill, Sairam S Mallajosyula, Göran Widmalm, Alexander D MacKerell, Jr.
  321 Computational analysis of a ring-opening reaction from an oxazolidine to an iminium cation
Antonios Marios N Chionis, M. C. Milletti.
  322 Computational analysis of activation barriers to C-C bond rotations for an iminium cation
Amanda Dewyer, M.C. Milletti
  323 Computational study of PAI-1 and its interactions with an inhibitor
Steve Spaulding, M.C. Milletti.
  324 Applying novel data mining techniques to create a new chemical database of environmental interest
Jun Zhang, Hao Zhu.
  325 Structures of sterically hindered metalloporphyrins and metallocorroles: Empirical dispersion corrections on optimized DFT geometries
Adam C Chamberlin, Abhik Ghosh
  326 Molecular interpretation of the barriers and minima of hydrophobic assembly
Brad A Bauer, Shuching Ou, Sandeep Patel.
  327 Vapor-liquid equilibria using Monte Carlo Wang-Landau simulations
Tsvetan Aleksandrov, Caroline Desgranges, Jerome Delhommelle.
  328 Towards more efficient enhanced sampling methods to study phase transitions
Kenneth Ndumbe Ngale, Caroline Desgranges, Jerome Delhommelle.
  329 Adsorption of carbon dioxide in IRMOFs using molecular simulations
Jason M. Hicks, Caroline Desgranges, Jerome Delhommelle.
  330 Molecular mechanisms for self-assembly in neurodegenerative diseases
Erica A. Hicks, Caroline Desgranges, Jerome Delhommelle
  331 Development of a multiple receptor docking protocol to account for sequence and conformational variability in DOCK
Brian C Fochtman, Trent E Balius, Sudipto Mukherjee, Patrick M Holden, Robert C Rizzo
  332 Characterization of peptide fusion inhibitors targeting HIV gp41 employing thermodynamic integration
Lingling Jiang, Robert C Rizzo.
  333 Structure-activity studies on antiproliferative factor (APF) glycopeptide derivatives
Sairam S Mallajosyula, Joseph J. Barchi, Kristie M. Adams, Alexander D MacKerell Jr.
  334 Development of homology model and active site identification for A/H1N1
Prashant R Murumkar, Pradeep N Gupta, Prasanna A Datar
  335 Characterization of electrostatic interactions in the denatured states of NTL9
Chuanyin Shi, Wei Chen, Jana K. Shen
  336 Computational approaches to modeling of TiO2 thin film photoelectrochemical cell
Stephanie J Jensen, Dmitri Kilin.
  337 Computational modeling of a colicin pore
Lidia Prieto, Themis Lazaridis
  338 High level quantum mechanical studies of singlet carbenes HCXH (X=O, S, Se)
Jean M. Standard
  339 Enhanced amyloidogenecity by histidine protonation in a truncation variant of β2-microglobulin
Chuanyin Shi, Jana K Shen.
  340 Computational modeling of TiO2 (001) anatase surfaces functionalized by transition metal doping
Yuchi Zhang, Dmitri Kilin
  341 Microporous molecular crystals: How to analyse the surface area of dynamic pores?
Mark A Lewis, Jelena Jordanovic, Abbie Trewin, Andy I Cooper
  342 RIng polymer dynamics in curved spaces
Sarah E Wolf, Emanuele Curotto.
  343 In silico mutagenesis of Rubisco using the protein local optimization program with comparisons against crystal structures
Edward B Miller, Richard A Friesner
  344 Substituent effects in a Lewis acid catalyzed aza-Cope Mannich tandem reaction
Alyssa Winkler, M.C. Milletti.
  345 Computational determination of trends contributing to Lewis basicity
Joseph J Rosmus, Jeffrey D Evanseck.
  346 Computational and experimental muon spin spectroscopy studies of the thermally mediated rearrangement of azulene into napthalene
Andrew K. Long, Cory C. Pye, Jason A. C. Clyburne, Brett M. McCollum, Jean-Claude Brodovitch, Paul W. Percival.
  347 Enhanced sampling in free energy calculations
Gerhard König, Benjamin T Miller, Stefan Boresch, Xiongwu Wu, Bernard R Brooks.
  348 Application of the electrostatically embedded many-body (EE-MB) approximation method to penta- and hexacoordinate zinc model systems
Elbek K Kurbanov, Hannah R Leverentz, Donald G Truhlar, Elizabeth A Amin
  349 Development and implementation of a variational reaction coordinate method
Adam B. Birkholz, H. B. Schlegel
  350 Relationships between graphs and atomic positions for generated 3D amorphous molecular fragments with cyclic structure
Steven G Arturo
  351 Predicting the low-lying excited states of ethylene and butadiene to chemical accuracy
Mark A Watson, Takeshi Yanai, Garnet K-L Chan
  352 Study of spanning water networks of hydration water in crowded protein solutions
Di Cui, Sandeep Patel.
  353 Spontaneous formation of micelle and bilayer in pH-sensitive surfactants
Brian H. Morrow, Peter H. Koenig, Jana K. Shen
  354 Functional classification of the six-hairpin glycosidase superfamily based on structurally aligned local active sites
Ramya Parasuram, Mary Jo Ondrechen
  355 Predictive enzyme catalysis and protein structure with quantum chemistry on the GPU
Heather J. Kulik, Todd J. Martinez.
  356 Potential of mean force calculations on base flipping of carcinogen-modified base in DNA duplexes
Bin Lin, Vipin Jain, Bongsup P. Cho, Alexander D. MacKerell, Jr.
  357 Investigations of the folding dynamics of the RNA pseudoknot structural motif via massively parallel molecular dynamics
Carolyn Kusaba, Benjamin Pham, Amethyst Radcliffe, Phuc La, Mona Bakhom, Richard Wang, Eric J Sorin.
  358 Molecular principles of coupled folding and binding
Sushant Kumar, William Noid.
  359 New method for induced fit docking (GENIUS) and its applicationto virtual screening of novel HCV NS3-4A protease inhibitors
Daisuke Takaya, Atsuya Yamashita, Kazue Kamijo, Junko Gomi, Masahiko Ito, Shinya Maekawa, Nobuyuki Enomoto, Naoya Sakamoto, Yoshiaki Watanabe, Ryoichi Arai, Hideaki Umeyama, Teruki Honma, Takehisa Matsumoto, Shigeyuki Yokoyama
  360 New method for induced fit docking (GENIUS) and its applicationto virtual screening of novel HCV NS3-4A protease inhibitors
Malela Werner, Zhiyu Li, Randy J Zauhar
  361 Molecular docking study based on pharmacophore modeling for novel phosphodiesterase IV (PDEIV) inhibitors
Gulsah Cifci, Viktorya Aviyente, Demet Akten
  362 Characterizing the binding of enzyme inhibitors at the molecular and ensemble levels
Samantha Cao, Benjamin Pham, Amethyst Radcliffe, Phuc La, Richard Wang, Eric Sorin.
  363 Describing the active-site motions and conformational changes of subtilisin Carlsberg in hexane during catalysis
Kristen A Marino, Aoife Fogarty, Damien Laage
  364 DNA triplex and the bisLNA construct
Mauricio Esguerra, Alessandra Villa, Lennart Nilsson.
  365 Understanding the role of many-body correlations in deriving accurate knowledge-based potentials
Joseph F Rudzinski, William G Noid
  366 Affordable scheme for including nuclear quantum effects in Metropolis Monte Carlo simulations: Tests of the displaced-points path integral method
Mohammadhasan Dinpajooh, Steven L Mielke, Donald G Truhlar, J. Ilja Siepmann
  367 Investigating a second-level of coding between RNA and protein structure in the HIV-1 genome
Amanda Westgate, Suzanne Szewczyk, Christian Laing, Henry Castejon.
  368 QTAIM analysis of the hydrogen bond network and atomic energies of substituted polyalanine α-helices
Laura Albrecht, David Hally, Russell J. Boyd.
  369 Transformations in the protein folding landscape by interfacial confinement
Apratim Bhattacharya, Jeetain Mittal.
  370 Functional assignment of structural genomics proteins in the ribulose-phosphate binding barrel superfamily
Joslynn S Lee, Mary Jo Ondrechen
  371 pKa calculations of protein side chains in explicit solvent using the classical drude polarizable force field
Xiao Zhu, Pedro Lopes, Alexander D MacKerell, Jr..
  372 Titratable residues in druggable binding sites: New insights for structure-based drug design
Jesus Seco Moral, Jana K. Shen
  373 Exploring the flexibility of the KIX domain of CREB binding protein and its interactions with transcriptional activator domains in silico
Jessica Gagnon, Charles Brooks III.
  374 Polarizable simulations with second order interaction model parameters for small molecules and dipeptides
Xinbi Li, Sergei Y. Ponomarev, George A. Kaminski
  375 Can physics-based docking approaches identify allosteric regulators of metabolic enzymes?
Adam H Steeves, Matthew P Jacobson
  376 Resources available from the 2011 CSAR benchmark exercise
Richard D Smith, Kelly L Damm-Ganamet, Jeanne A Stukey, Emilio Xavier Esposito, James B Dunbar Jr., Heather A Carlson
  377 Molecular simulations of interaction between inorganic phosphate and collagen
Rachel M Gill, Adriana Dinescu.
  378 Effects of the midspan arginine-to-leucine mutation on the conformational distribution of the HIV-1 gp41 membrane spanning domain
Michelle Baker, Vamshi K. Gangupomu, Cameron F. Abrams.
  379 Accurate molecular dynamics simulation of peptide adsorption to polyethylene, poly(methyl-methacrylate), and silica surfaces using dual-force-field in CHARMM
Tigran Abramyan, James Snyder, Jeremy Yancey, Steven J. Stuart, Robert A. Latour.
  380 Vibronic coupling simulations: Applications to linear and nonlinear optical processes
Daniel W. Silverstein, Lasse Jensen.
  381 Identification of potential binding sites of known non-competitive inhibitors of N5-CAIR synthetase
Sebastien Hebert, Venkatta S Pakkala, Jeffery D Evanseck, Steven M Firestine
  382 Molecular dynamics studies of small ion channels: Linking structure and conductance
Thuy Hien T Nguyen, Michael A Wilson, Chenyu Wei, Andrew Pohorille.
  383 Molecular dynamics studies on bilayer perturbations comprised of homo-oligomeric bundles
Thuy Hien T Nguyen, Zhiwei Liu, Preston B Moore
  384 Open chemistry: Realizing open data, open standards, and open source
Kyle Lutz, Marcus D Hanwell, Chris Harris, David Cole.
  385 Accurate modeling of peptide-surface interactions: Interfacial force field parameterization for organic functional groups
Nadeem Ahmad Vellore, Jeremy A Yancey, Steven J Stuart, Robert A Latour
  386 Accounting for induced polarization in non-polarizable force fields
Igor Leontyev, Alexei Stuchebrukhov.
  387 Validation of a constant pH molecular dynamics implementation in an explicit solvent
Jeffrey P Hafner, Jason A Wallace, Jana K Shen.
  388 Structure of water at charged surfaces: A molecular picture
Shalaka Dewan, Ali Eftekhari-Bafrooei, Vincenzo Carnevale, Giacomo Fiorin, Michael L Klein, Eric Borguet.
  389 Molecular dynamics and quantum methods probe aerospace materials
Samuel J Tucker, Andrea R Browning, Kady Gregersen, Stephen Christensen.
  390 Identifying TRPV1 modulators by structure-based virtual screening: A case study of using drug discovery tools at mcule.com
Ferenc Szalai, László Kovács, Zoltán Oláh, Róbert Kiss.
  391 Integration strategies for virtual and experimental screening. A case study on c-Jun N-terminal kinase 3 (JNK3)
Róbert Kiss, György M Keserű.
  392 Theoretical study of the NO2 decomposition over a modified Cu-FAU zeolite
Tianxiang Liu, A. William Barber, Heriberto Hernandez-Soto
  393 Shape similarity based approach towards the development of new HCV translation inhibitors
Kejia Ding, Thomas Hermann.
  394 Entropic and intramolecular polarization effects in catalytic mechanism of Cyclophilin A
Safieh Tork Ladani, Donald Hamelberg.
  395 Thermochemical analysis of two small fast-folding proteins using coarse-grained simulation
Frank C Pickard, Benjamin T Miller, Bernard R Brooks.
  396 Linear basis function approaches to efficient free energy calculations
Levi N Naden, Tri T Pham, Michael R Shirts.
  397 Introducing charge hydration asymmetry into the realm of continuum solvation: The Born equation revisited
Abhishek Mukhopadhyay, Andrew T Fenley, Igor Tolokh, Alexey A Onufriev
  398 Contribution to affinity from quantum resonance: A fragment-based approach to RecA and PCSK9
John L Kulp III, John L Kulp Jr., Frank K Guarnieri.
  399 Applications of GPU-accelerated replica exchange molecular dynamic simulations of proteins
Kai Wang, Michael R. Shirts
  400 How to get ion-ion PMF in implicit water right?
Igor S Tolokh, Lois Pollack, Nathan Baker, Alexey A Onufriev.
  401 Interfacial properties of guanidinium and methyl guanidinium solutions studied using CHARMM polarizable charge equilibration force fields
Timothy R Lucas, Shuching Ou, Sandeep Patel.
  402 Using molecular similarity to reduce the cost of electronic structure calculations
Matteus Tanha, Shiva Kaul, Geoffrey J. Gordon, David Yaron.
  403 Study of drug-lipid interactions by molecular dynamic simulations of phenobarbital in lipid bilayer
Jacky Wang, Preston B Moore, Thuy Hien T. Nguyen, Zhiwei Liu.
  404 Q-chem 4.0 program: Frontiers of quantum modeling
Jing Kong, Yihan Shao.
  405 Modeling protein transport in charged chromatographic gels using coarse-grained molecular dynamics simulation
Joseph Basconi, Michael R. Shirts
  406 "Market basket" analysis applied to pharmacophore features: Constructing topological pharmacophores
Paul J Kowalczyk
  407 Why are crystallographic water molecules crystallographic?
Hongwei Tan, Nader Nasief, David Hangauer, Thomas Furlani, Jing Kong.
  408 Molecular docking and in silico structure-based design of D-(X)-Pro-D-Arg-derived direct thrombin inhibitors
Cristina C Clement, Janet Gonzalez, Manfred Philipp.
  409 Insight on the binding mode of glucocorticoid ligands
Anna Maria Capelli, A Bruno, G Costantino.
  410 Development and experimental validation of a 2D fingerprint method to improve virtual screening enrichments
James I Fells, Sue Chin Lee, Ryoko Tsukahara, Jianxiong Liu, Jason Kirby, Sandra Nelson, Gabor Tigyi.
  411 Predictive toxicity protocol for cell-viability high throughput data
Sing-zuo Chen, Bo-Han Su, Yufeng Jane Tseng.
  412 Combined approach of stochastic potential surface and car-Parinello simulated annealing simulation for searching for stable SinCn clusters
Xaiofeng F Duan, Larry W Burggraf, Lingyu Huang
  413 Why different binding channels in one catalytic site? Unraveling how FAAH induces prereactive conformations of its flexible substrates
Giulia Palermo, Pablo Campomanes, Marilisa Neri, Daniele Piomelli, Andrea Cavalli, Ursula Rothlisberger, Marco De Vivo.
  414 Rational computationally-driven design of novel molecular materials: Organic piezoelectrics and photovoltaics for energy applications.
Geoffrey R Hutchison.
  415 Use of GEM distributed multipoles for the AMOEBA force field
G. Andrés Cisneros
  416 Robust, transferable, and physically-motivated force fields for gas adsorption in nanoporous systems
Jesse G McDaniel, Kuang Yu, J. R. Schmidt.
  417 Electronic structure of Pt13H24 cluster and its surface chemistry
Qingguo Meng, P Stanley May, Mary T Berry, Dmitri Kilin.
  418 Ras nanoclusters and membrane domains
Alemayehu A Gorfe
  419 Water-based mechanism of specificity and resistance for lapatinib with ErbB family kinases
Yulin Huang, Robert C Rizzo.
  420 Charge separation propensity of coenzyme B12–tyrosine complex: PCET–induced enzymatic catalysis in methylmalonyl–CoA mutase enzyme
Neeraj Kumar, Pawel M Kozlowski.
  421 Abstraction energy controls catalytic activity of palladium nanocrystals in atom leaching carbon-carbon coupling reactions
Hadi Ramezani-Dakhel, Peter A Mirau, Rajesh R Naik, Marc R Knecht, Hendrik Heinz.
  422 Dr-predictor: Predicting cytochrome P450 metabolism by combining flexible docking and reactivity calculation with multiple instance ranking
Tao-Wei Huang, Jed Zaretzki, Charles Bergeron, Kristin Bennett, Curt Breneman.
  423 Understanding the molecular mechanisms underlying the application of combination therapies to inhibit the Hepatitis C virus polymerase
Jodian A. Brown, Ian F. Thorpe.
  424 Parallel QM/MM X-ray refinement of protein bound anti-Alzheimer drug donepezil
Zheng Fu, Xue Li, Yipu Miao, Kenneth M Merz, Jr.
  425 QSARs for the removal of endocrine disrupting compounds from waste water
Lisa N. Morkowchuk, Alison R. Kennicutt, James E. Kilduff, Curt M. Breneman.
  426 Redox energetics of hypercloso boron hydrides BnHn (n=6-13) and B12X12 (X=F, Cl, OH, and CH3)
Taebum Lee
  427 Applications of molecular modeling and Computer-Aided Drug Design (CADD) to inhibit biological targets in prostate cancer
Eleonora Gianti, Marja T. Nevalainen, Vincent C.O. Njar, Randy J. Zauhar.
  428 Assessment of RNA force field performance by comparison of MD simulations to solution NMR data
Niel M Henriksen, Thomas E Cheatham.
  429 Novel simulation methods for studying modulated phases
Kai Zhang, Patrick Charbonneau.
  430 Investigation of peptide inhibitors of Clostridium difficile toxin B: Differentiating between mechanisms by computational methods, functionalizing to irreversibility
Rebecca J Swett, G. Andres Cisneros, Andrew L Feig.
  431 Rationalization and visualization of nonbonded interactions
Elizabeth Sourial.
  432 Efficient data mining of the human kinome
Nels Thorsteinson

WEDNESDAY MORNING

Pennsylvania Convention Center
Room 117

Drug Discovery - Target-based Cosponsored by BIOL, CINF, MEDI
Scott Wildman, Y. Jane Tseng, Organizers
Katrina Lexa, Presiding
8:30 463 Interaction of avibactam with OXA-48 and KPC-2 carbapenemases accounts for its unique efficiency in the treatment of antibiotic resistance
Thierry Naas, Cédrik Brozek, Guillaume Bernadat, Oliver Beckstein, Patrice Nordmann, Bogdan I Iorga.
9:00 464 Computer-aided drug design (CADD) to discover novel inhibitors of protein targets in prostate cancer
Eleonora Gianti, Marja T. Nevalainen, Vincent C.O. Njar, Randy J. Zauhar.
9:30 465 Lead identification of viral entry inhibitors targeting HIVgp41
Patrick Holden, Harmeet Kaur, Rashi Goyal, Miriam Gochin, Robert C Rizzo
10:00 466 Molecular modeling studies of the human GABA transporter 1: Insights into binding events of Tiagabine analogs
Barbara Zdrazil, Andreas Jurik, Stine B Vogensen, Harald H Sitte, Gerhard F Ecker
10:30   Intermission.
10:45 467 Identifying novel JAK1 inhibitors by structure-based virtual screening: A case study of using drug discovery tools at mcule.com
Robert Kiss, Ferenc Szalai, Peter P Sayeski, György M Keserű
11:15 468 Structure-based identification of multitarget FAAH/COXs inhibitors: Tackling inflammation with a single molecule acting on multiple proteins
Angelo D Favia, Damien Herbrant, Marco Migliore, Mauro Dionisi, Clara Albani, Glauco Tarozzo, Daniele Piomelli, Rita Scarpelli, Andrea Cavalli, Marco De Vivo.
11:45 469 Information for rescoring protein-drug binding
Shijun Zhong

Pennsylvania Convention Center
Room 116

Molecular Mechanics - Applications Cosponsored by BIOL, CINF, MEDI, PHYS
Michael Feig, Organizer
Yulin Huang, Presiding
8:30 458 Molecular basis of Xe affinities for water soluble cryptophanes
Lu Gao, Christopher Von Bargen, Ivan J Dmochowski, Jeffery G Saven
9:00 459 Dynamic porosity as a key feature of microporous soft organic molecular crystals
Jelena Jordanovic, Mark A Lewis, Tamoghna Mitra, Abbie Trewin, Andy I Cooper
9:30 460 Enantioselective binding of additives to chiral crystals
Damien J Carter, Bart Kahr, Andrew L. Rohl.
10:00   Intermission.
10:15 461 Molecular dynamics study of hydrocarbon diffusion and hydrocarbon cracking reactions in zeolites
Kaushik L Joshi, Adri van Duin.
10:45 462 Modeling the competing pathways involved in catalytic cracking of hydrocarbon fuels via the ReaxFF reactive force field
Fidel Castro-Marcano, Adri C. van Duin.

Pennsylvania Convention Center
Room 118 B

Perspectives in Applied Computational Methods Cosponsored by BIOL, CINF, MEDI
Cynthia Bancale, Raul Alvarez, Carsten Detering, Organizers
9:00   Introductory Remarks
9:05 476 It's just like a nightclub: Posing and scoring with OEDocking
Paul Hawkins, Gregory Warren.
9:50 477 Computational chemistry opportunities in early drug discovery
Sabine Ruppel
10:35   Intermission.
10:55 478 Systematic study of the ligand strain energy derived from the quantum mechanics crystallographic refinement using the linear scaling program DivCon integrated into the PHENIX package
Oleg Y Borbulevych, Joshua A Plumley, Lance M Westerhoff.

WEDNESDAY AFTERNOON

Pennsylvania Convention Center
Room 116

Molecular Mechanics - Applications Cosponsored by BIOL, CINF, MEDI, PHYS
Michael Feig, Organizer
Sajeewa Walimuni Dewage, Presiding
1:30 504 Computational modeling of peptoid folding
Vincent A Voelz
2:00 505 Conformational control of aromatic oligoamide foldamers: Predicting oligomer structures in solution through molecular dynamics simulations
Zhiwei Liu, Jhenny F. Galan, Chi-Ngong Tang, Jessica A. Geer, Shubhashis Chakrabarty, Eduardo M. Sproviero, Guillermo Moyna, Vojislava Pophristic.
2:30 506 Building helical aromatic oligoamide foldamers
Jessica A Geer, Zhiwei Liu, Eduardo Sproviero, Vojislava Pophristic
3:00   Intermission.
3:15 507 Molecular dynamics investigation of DNA-binding foldamers
Ara Abramyan, Zhiwei Liu, Vojislava Pophristic
3:45 508 Conformational analysis of nucleosides: A systematic update of PSEUROT using quantum mechanical- and molecular mechanics-derived parameters
Rodney Agnant, Kevin M. Ileka, Steven M. Graham
4:15 509 Specific and nonspecific effects of N-linked glycosylation
Christopher R Ellis, William G Noid.

Pennsylvania Convention Center
Room 118 B

Perspectives in Applied Computational Methods Cosponsored by BIOL, CINF, MEDI
Cynthia Bancale, Raul Alvarez, Carsten Detering, Organizers
2:00   Introductory Remarks
2:05 521 Machine learning: "Better practices" applied to antimalarial drug discovery
Paul J Kowalczyk
2:50   Intermission.
3:10 522 Improving potency and ADMET properties using matched molecular pair analysis
David W Miller
3:55 523 Stifling of large pharma innovation through institutionalized mediocrity: Consultants, gatekeepers, and uncrowned kings
Andrew Good

Pennsylvania Convention Center
Room 118 A

Simulations of Crowding, Confinement, and Cellular Environments Cosponsored by BIOL, CELL, CINF, COLL, MEDI, PHYS
Michael Feig, Organizer
Sajeewa Walimuni Dewage, Presiding
1:30 515 Simulations of the folding and dynamics of proteins under confinement
Angel E Garcia, Jianhui Tian.
2:10 516 Computational studies of actin folding within cylindrical nanopores
George Stan, Pooja Shrestha, Nathan Smith.
2:50 517 Simulation of proteins and synaptic vesicles under external potentials
Martin E. Garcia
3:30 518 Dynamics of proteins in confined and crowded spaces: Insights from Go-like models
Marek Cieplak
4:10   Intermission.
4:25 519 Protein folding and aggregation on surfaces
Joan Shea
5:05 520 Simulations of biomolecular assembly processes at interfaces
Jeetain Mittal

Pennsylvania Convention Center
Room 117

Understanding and Predicting the Role of Water in Drug Design Cosponsored by BIOL, CINF, MEDI, PHYS
Jean-Francois Truchon, Vijay Pande, Raul Alvarez, Organizers
1:30 510 Mapping and using active site water structures and energetics via WaterMap: Lead discovery, lead optimization, and physical insight
Richard A Friesner
2:00 511 Use of 3D-RISM for water analysis in drug design
Jean-François Truchon, Paul Labute
2:30 512 Using water to probe binding sites: Designing ligands with SZMAP
Matthew T Geballe, J. Michael Word, A. Geoffrey Skillman, Anthony Nicholls.
3:00   Intermission.
3:15 513 Water water everywhere but not a drop to drink: The use of water site mapping tools for structure-based drug design
Alan P Graves
3:45 514 Using solvent-mapping calculations for virtual screening
Demetri T Moustakas

THURSDAY MORNING

Pennsylvania Convention Center
Room 115 C

Drug Discovery - Structural Bioinformatics Cosponsored by BIOL, CINF, MEDI
Scott Wildman, Y. Jane Tseng, Organizers
William Allen, Presiding
8:30 535 Voronoi interaction propensities from the PDB - harnessing 100 million non-covalent interactions
Fred Ludlow
9:00 536 Accurate prediction of hydrogen bond networks in protein-ligand complexes
Carsten Detering, Tobias Lippert, Matthias Rarey, Holger Claussen.
9:30 537 Using QM/MM X-ray refinement approach in drug discovery
Zheng Fu, Xue Li, Kenneth M Merz, Jr.
10:00   Intermission.
10:15 538 Identification and evaluation of the binding hotspots at the protein-protein interaction interfaces using the cosolvent molecular dynamics simulation and cosolvent mapping analysis
Chao-Yie Yang, Shaomeng Wang.
10:45 539 High throughput identification of protein binding sites
Sandor Vajda, Dima Kozakov, Chi Ho Ngan, Brandon Zerbe, Tanggis Bohnuud.
11:15 540 Peptides derived from the recognition helices of the gal and lac repressor proteins demonstrate sequence-specific DNA-binding
Suliman Salman, Daniel A. Barr.

Philadelphia Marriott Downtown
Salon G

Understanding and Predicting the Role of Water in Drug Design Cosponsored by BIOL, CINF, MEDI, PHYS
Jean-Francois Truchon, Raul Alvarez, Vijay Pande, Organizers
8:30 541 Structural studies of putative water-binding sites in proteins
Brian W. Matthews
9:00 542 Statistical-mechanical, 3D molecular theory of solvation predicts the role of water in soft matter and biomolecular systems
Andriy Kovalenko
9:30 543 Localized thermodynamics of active site solvation from grid inhomogeneous solvation theory (GIST)
Tom Kurtzman Young, Crystal Nguyen, Michael K Gilson.
10:00   Intermission.
10:15 544 Testing and assembling the response of water at molecular interfaces
Christopher J Fennell, Libo Li, Charles W Kehoe, Ken A Dill.
10:45 545 Fluctuations in water, the hydrophobic effect and self-assembly
Patrick S Varilly, Amish J Patel, Sumanth N Jamadagni, Hari Acharya, Michael F Hagan, Shekhar Garde, David Chandler, Tuomas P J Knowles, Daan Frenkel

 

SCHB Symposia
Cosponsored by CINF

Joseph Sabol, Program Chair

MONDAY MORNING

Philadelphia Downtown Courtyard by Marriott
Grand Ballroom Salon I&II

What You Need To Know About the New U.S. Patent Laws Cosponsored by CEPA, CINF, PROF, YCC
Jeffrey Bergman, Organizer, Presiding
8:30   Introductory Remarks.
8:35 12 Costs under AIA
Connie Pielech
9:05 13 Post-grant procedures under the AIA
Jeffrey Bergman
9:35 14 Recent patent law decisions and updates on patent law
Mike Locklar
10:05   Intermission.
10:20 15 Joinder and venue changes under the AIA
Steve Schlather
10:50 16 AIA's effect on patenting strategies
Clif McCann
11:20 17 AIA's effect on patent litigation and dispute resolution strategies
Clif McCann
11:50   Concluding Remarks.