Technical Program Listing

ACS Chemical Information Division (CINF)
245th ACS National Meeting, Spring 2013
New Orleans, LA (April 7 - 11)

CINF Symposia

J. Garritano, Program Chair

Sunday, April 7, 2013 8:30 am - 11:50 am

Advances in Visualizing and Analyzing Biomolecular Screening Data - AM Session Data-Mining Public Bioactivity Data
Morial Convention Center
Room: 349
Cosponsored by COMP
Deepak Bandyopadhyay, Jun Huan, Organizers
Deepak Bandyopadhyay, Jun Huan, Presiding
8:30   Introductory Remarks
8:35 1 Characterizing the diversity and biological relevance of the MLPCN assay manifold and screening set

Jun Huan, jhuan@ittc.ku.edu,
Abstract

9:00 2 New ways to mine disparate screening data in PubChem

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

9:25 3 PubChem DataDicer: A data warehouse for rapid querying of bioassay data

Lewis Y Geer, lewisg@ncbi.nlm.nih.gov, Lianyi Han, Siqian He, Yanli Wang, Evan E Bolton, Stephen H Bryant.
Abstract

9:50 4 PubChem widgets

Lianyi Han, hanl@ncbi.nlm.nih.gov,
Abstract

10:15   Intermission
10:35 5 Automated structure-activity relationship mining: Connecting chemical structure to biological profiles

Mathias Wawer1, mwawer@broadinstitute.org, David Jaramillo1, Kejie Li1, Sigrun Gustafsdottir1, Vebjorn Ljosa4, Nicole Bodycombe1, Melissa Parkin3, Katherine Sokolnicki4, Mark-Anthony Bray4, Ellen Winchester3, George Grant3, Cindy Hon1, Jeremy Duvall2, Joshua Bittker2, Vlado Dancik1, Rajiv Narayan5, Aravind Subramanian5, Wendy Winckler3, Todd Golub5, Anne Carpenter4, Stuart Schreiber1, Alykhan Shamji1, Jürgen Bajorath6, Paul Clemons1.
Abstract

11:00 6 Using the bi-clustering SPE for the visualization and analysis of massive amounts of compound-target activity data

Dmitrii Rassokhin1, drassokh@its.jnj.com, Dimitris Agrafiotis2, Eric Yang2.
Abstract

11:25 7 BioAssay Research Database: A platform to support the collection, management, and analysis of chemical biology data

Rajarshi Guha1, guhar@mail.nih.gov, David Lahr2, Joshua Bittker2, Thomas D.Y. Chung3, Mark Southern7, Simon Chatwin2, Jeremy J Yang4, Oleg Ursu4, Christian G Bologa4, Tudor I Oprea4, Eric Dawson5, Shaun R Stauffer5, Craig W Lindsley5, Uma Vempati6, Hande Kucuk6, Stephan C Schurer6, Stephen Brudz2, Paul A Clemons2, Andrea de Souza2, Noel Southall1, Dac-Trung Nguyen1, John Braisted1, Tyler Peryea1.
Abstract

Sunday, April 7, 2013 8:20 am - 11:45 am

Library Cafes, Intellectual Commons and Virtual Services, Oh My! Charting New Routes for Users into Research Libraries - AM Session Transforming Libraries
Morial Convention Center
Room: 350
Cosponsored by CHED
Leah Solla, Olivia Bautista Sparks, Teri Vogel, Organizers
Leah Solla, Teri Vogel, Presiding
8:20   Introductory Remarks
8:25 8 Transformation of academic branch libraries

Nevenka Zdravkovska, nevenka@umd.edu,
Abstract; Presentation (pdf)

8:50 9 Library spaces for scientific computing discovery and learning

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

9:15 10 Heart of the university or how to stay stuck in the middle with you

Susanne J Redalje, curie@uw.edu, Lauren Ray.
Abstract; Presentation (pdf)

9:40 11 From traditional library organization to functional structure: How does it benefit library users?

Erja Kajosalo, kajosalo@mit.edu,
Abstract; Presentation (pdf)

10:05   Intermission
10:20 12 Holistic approaches to service: Connecting researchers to libraries through relationship building

Kiyomi D. Deards, Kdeards2@unl.edu,
Abstract

10:45 13 Ask for research alterations: Emerge with a custom fit

Jill E Wilson, jew248@cornell.edu, Leah R McEwen.
Abstract

11:10 14 Let's work together: ACS Publications author outreach initiatives and opportunities for libraries

Sara Rouhi, S_Rouhi@acs.org,
Abstract; Presentation (pdf)

Sunday, April 7, 2013 2:00 pm - 5:15 pm

Advances in Visualizing and Analyzing Biomolecular Screening Data - PM Session Tools, Techniques, Platforms and Software
Morial Convention Center
Room: 349
Cosponsored by COMP
Deepak Bandyopadhyay, Jun Huan, Organizers
Deepak Bandyopadhyay, Jun Huan, Presiding
2:00 15 3D phylogenetic trees for visualization and analysis of complex datasets

Ruben Abagyan1,2, k6wright@ucsd.edu, Eugene Raush2, Maxim Totrov2.
Abstract

2:25 16 On-line graph mining and visualization of protein-ligand interactome

Clara Ng1, lxi0003@hunter.cuny.edu, Lei Xie1,2, lxi0003@hunter.cuny.edu.
Abstract

2:50 17 Encoded Library Technology data analysis: Finding the grain of sand you want without getting a sunburn

Kenneth E Lind, kenneth.e.lind@gsk.com, Neil R Carlson, Ninad V Prabhu, Jeff A Messer.
Abstract

3:15   Intermission
3:35 18 Exploring the chemical space of screening results

Ed Champness, ed@optibrium.com, Matt Segall, Chris Leeding, James Chisholm, Iskander Yusof, Hector Martinez, Nick Foster.
Abstract

4:00 19 How to highlight hits: Advances in visual data analytics tools for HTS data

Jesse A. Gordon, jesse.gordon@dotmatics.com, Jess Sager.
Abstract

4:25 20 Integrated cheminformatics software for visualizing and analyzing high-throughput screening data

Denis Fourches, fourches@email.unc.edu, Alexander Tropsha.
Abstract

4:50 21 Integrating design, analysis, and visualization into the drug discovery workflow

W. Patrick P. Walters1, pat_walters@vrtx.com, Carlos Faerman1, Jonathan Weiss1, Xiaodan Zhang1, Roslyn Potter1, Jun Feng1, Guy Bemis1, Susan Roberts2, Jason Yuen2, Trevor Kramer2, Jonathan Christopher3, Jeff Orr3, Brian Goldman1.
Abstract

Sunday, April 7, 2013 2:30 pm - 5:00 pm

Library Cafes, Intellectual Commons and Virtual Services, Oh My! Charting New Routes for Users into Research Libraries - PM Session Online Tools
Morial Convention Center
Room: 350
Cosponsored by CHED, COMP
Leah Solla, Teri Vogel, Olivia Bautista Sparks, Organizers
Leah Solla, Teri Vogel, Presiding
2:30   Introductory Remarks
2:35 22 Cambridge Structural Database: Moving with the times

Susan Henderson, henderson@ccdc.cam.ac.uk, Ian J Bruno.
Abstract; Presentation (pdf)

3:00 23 ChemEd DL WikiHyperGlossary: A social semantic information literacy service for digital documents

Robert E. Belford1, rebelford@ualr.edu, Dan Berleant2, Michael A. Bauer2, Jon L. Holmes3, John W. Moore3.
Abstract; Video presentation (.avi)

3:25 24 Navigating scientific resources using wiki-based resources

Antony J Williams1, williamsa@rsc.org, Valery Tkachenko1, Alexey Pshenichnov1, Sean Ekins3, Aileen Day2, Martin Walker4.
Abstract; Presentation

3:50 25 CuLLR me collaboration: Models and tools for user-driven eLibraries

Dianne Dietrich, dd388@cornell.edu, Leah R McEwen.
Abstract

Sunday, April 7, 2013 6:30 pm - 8:30 pm

CINF Scholarship for Scientific Excellence - EVE Session
Morial Convention Center
Room: 343
Guenter Grethe, Organizers
, Presiding
  26 iBIOMES: Managing and sharing large biomolecular simulation datasets in a distributed environment with iRODS

Julien C Thibault1, julien.thibault@utah.edu, Thomas E Cheatham2,3, Julio C Facelli1,3.
Abstract

27 Probing the substrate selectivity of the serotonin and dopamine transporter using structure based techniques

Amir Seddik1, amir.seddik@univie.ac.at, Harald H. Sitte2, Gerhard F. Ecker1.
Abstract

28 New cheminformatics microscopes: Combining semantic web technologies, cheminformatical representations, and chemometrics for understanding and predicting chemical and biological properties

Egon L Willighagen, egon.willighagen@maastrichtuniversity.nl,
Abstract

29 Discovery of TLR2 antagonists by virtual screening

Manuela S Murgueitio1, m.murgueitio@fu-berlin.de, Sandra Santos-Sierra2, Gerhard Wolber1.
Abstract

Monday, April 8, 2013 8:30 am - 11:55 am

Advances in Visualizing and Analyzing Biomolecular Screening Data - AM Session Experimental Insights, Case Studies, and New Methods
Morial Convention Center
Room: 349
Cosponsored by COMP
Deepak Bandyopadhyay, Jun Huan, Organizers
Deepak Bandyopadhyay, Jun Huan, Presiding
8:30   Introductory Remarks
8:35 30 Dispensing processes profoundly impact biological assays and computational and statistical analyses

Sean Ekins1, ekinssean@yahoo.com, Joe Olechno2, Antony J Williams3.
Abstract

9:00 31 On the compound annotation and cleaning the GSK screening collection initiative: The utility of an Inhibition Frequency Index (IFI)

Subhas J Chakravorty, subhas.j.chakravorty@gsk.com, James A Chan, Juan Luengo, Nicole M Greenwood, Ioana Popa-Burke, Ricardo Macarron.
Abstract

9:25 32 Analyzing screening and similarity searching outcome in light of multiple approaches to the same target

Tina Garyantes, garyante@optonline.net,
Abstract

9:50   Intermission
10:10 33 Sharing chemical information from screens without revealing structures

S. Joshua J. Swamidass1, swamidass@gmail.com, Matthew Matlock1, Dimitris K. Agrafiotis2.
Abstract

10:35 34 Characterization and visualization of compound combination responses in a high throughout setting

Rajarshi Guha, guhar@mail.nih.gov, Lesley Mathews, John Keller, Paul Shinn, Craig Thomas, Anton Simeonov, Marc Ferrar.
Abstract

11:00 35 Characterizing activity landscapes using network-like similarity graphs to mine antibacterial data

Veerabahu Shanmugasundaram1, veerabahu.shanmugasundaram@pfizer.com, Steven Heck1, Justin Montgomery1, Preeti Iyer2, Dilyana Dimova2, Jürgen Bajorath2.
Abstract

11:25 36 From hits to leads: Data visualization of chemical scaffolds beyond traditional SAR exploration

Tyler Peryea, tyler.peryea@nih.gov, John Braisted, Ajit Jadhav, Rajarshi Guha, Noel Southall, Dac-Trung Nguyen.
Abstract

11:50   Concluding Remarks

Monday, April 8, 2013 8:10 am - 11:30 am

Scholarly Communication: New Models, New Media, New Metrics - AM Session
Morial Convention Center
Room: 350
David Martinsen, William Town, Colin Batchelor, Organizers
David Martinsen, Presiding
8:10   Introductory Remarks
8:15 37 Evolution of ACS DivCHED CCCE ConfChem: Gopher servers to the social semantic web

Robert E Belford1, rebelford@ualr.edu, Nitin Agarwal2, Steven Leimberg2, Jon L. Holmes3.
Abstract

8:45 38 Data enhancing the RSC Archive

Colin Batchelor1, batchelorc@rsc.org, Ken Karapetyan2, Alexey Pshenichnov2, David Sharpe1, Jon Steele1, Valery Tkachenko2, Antony Williams2.
Abstract

9:15 39 NIST-journal cooperation to improve the quality of published experimental data: Pre-acceptance evaluation and on-line tools

Robert D. Chirico1, robert.chirico@nist.gov, Michael Frenkel1, Joseph W. Magee1, Vladimir V. Diky1, Kenneth Kroenlein1, Chris D. Muzny1, Andrei F. Kazakov1, Ilmutdin M. Abdulagatov1, Gary R. Hardin1, Theodoor W. de Loos2, John P. O'Connell3, Clare McCabe4, Joan F. Brennecke5, Paul M. Mathias6, Anthony R. H. Goodwin7, Jiangtao Wu8, Kenneth N. Marsh9, Ronald D. Weir10, William E. Acree, Jr.11, Agilio Pádua12, W. M. (Mickey) Haynes1, Daniel G. Friend1, Andreas Mandelis13, Vicente Rives14, Christoph Schick15, Sergey Vyazovkin16, Ella Chen17.
Abstract

9:45   Intermission
10:00 40 Reproducibility in cheminformatics and computational chemistry research: Certainly we can do better than this

Gregory A. Landrum, Gregory.Landrum@novartis.com,
Abstract

10:30 41 Reproducible research applied to cheminformatics experiments

Paul J Kowalczyk, paul.kowalczyk@scynexis.com,
Abstract

11:00 42 Mythbusting scientific knowledge transfer with nanoHUB.org: Collaborative research and dissemination with quantifiable impact on research and education

Gerhard Klimeck, gecko@purdue.edu,
Abstract

Monday, April 8, 2013 1:30 pm - 5:30 pm

FoodInformatics: Applications of Chemical Information to Food Chemistry - PM Session
Morial Convention Center
Room: 349
Cosponsored by AGFD
Jose Medina-Franco, Karina Martinez Mayorga, Organizers
Jose Medina-Franco, Presiding
1:30   Introductory Remarks
1:35 43 Soft and fuzzy approach to food informatics

Gerald M Maggiora, gerry.maggiora@gmail.com,
Abstract

2:00 44 Exploring the chemical space of flavors and fragrances with the chemical universe database

Jean-Louis Reymond1, jean-louis.reymond@ioc.unibe.ch, Lars Ruddigkeit1, Mahendra Awale1, Guillaume Godin2.
Abstract

2:25 45 Tracing pharmacophore determinants of natural- and nutritional-like components in epigenetics and metabolism

Alberto Del Rio, alberto.delrio@gmail.com,
Abstract

2:50 46 Reverse pharmacognosy: From molecules to active ingredients

Quoc Tuan Do, quoctuan.do@greenpharma.com, Sylvain Blondeau, Philippe Bernard.
Abstract

3:15 47 Flavor network: Exploring the principles of food pairing

Sebastian E Ahnert1, sea31@cam.ac.uk, Yong-Yeol Ahn2, Albert-Laszlo Barabasi3.
Abstract

3:40   Intermission
3:50 48 USP reference standards as value-added information sources in the Food Chemicals Codex (FCC)

Christina L. Cole, clc@usp.org,
Abstract

4:15 49 Reaxys as an information resource for food chemistry

David Evans1, david.evans@reedelsevier.ch, Juergen Swienty-Busch2.
Abstract

4:40 50 Profiling the trace metal composition of wine as a function of storage temperature and packaging type

Helene Hopfer1,2, hhopfer@ucdavis.edu, Jenny Nelson3, Carolyn L Doyle1,2, Hildegarde Heymann1, Alyson E. Mitchell2,4, Susan E. Ebeler1,2.
Abstract

5:05 51 Mining the protein space to determine prevalence of fragments identical with allergenic epitopes - chicken egg protein fragments as an example

Piotr Minkiewicz, minkiew@uwm.edu.pl, Monika Protasiewicz, Małgorzata Darewicz, Karolina Hurman, Anna Iwaniak.
Abstract

Monday, April 8, 2013 1:00 pm - 5:30 pm

Scholarly Communication: New Models, New Media, New Metrics - PM Session
Morial Convention Center
Room: 352
Cosponsored by YCC
William Town, Colin Batchelor, David Martinsen, Organizers
Colin Batchelor, William Town, Presiding
1:00   Introductory Remarks
1:05 52 Supplementary journal article materials: Summary of the NISO/NFAIS recommendations

David P Martinsen, d_martinsen@acs.org,
Abstract

1:35 53 Digital research that is discoverable, citable, and linked to primary research literature: The Data Citation Index

Daphne Grecchi, Daphne.Grecchi@thomsonreuters.com,
Abstract

2:05 54 From inception to collaboration to publication: A complete integrated research management platform for researchers

Judy Chen, j_chen@acs.org,
Abstract

2:35   Intermission
2:50 55 Evolving with our community: The RSC's approach to the challenges and opportunities of scientific communication

Richard Kidd, kiddr@rsc.org, James Milne.
Abstract

3:20 56 We're not in Kansas anymore

Roger Schenck, rschenck@cas.org,
Abstract

3:50 57 Challenging, cajoling, and rewarding the community for their contributions to online chemistry

Antony J Williams1, tony27587@gmail.com, Valery Tkachenko1, Alexey Pshenichnov1, Will Russell2, Jack Rumble2, David Leeming2.
Abstract

4:20   Intermission
4:30 58 Science comedian's guide to communicating science to general audiences

Brian Malow, brian.malow@naturalsciences.org,
Abstract

Monday, April 8, 2013 1:15 pm - 5:15 pm

Food for Thought: Alternative Careers in Chemistry - PM Session
Morial Convention Center
Room: 350
Cosponsored by PROF, YCC
Donna Wrublewski, Patricia Meindl, Organizers
Patricia Meindl, Presiding
1:15   Introductory Remarks
1:20 59 From studying block copolymers to chemical information: A journey of an alternative chemistry career as an academic science librarian

Vincent F Scalfani, vfscalfani@ua.edu,
Abstract

1:50 60 Successful careers in science: Why moving away from the bench brings you closer to advancing research

Lily Khidr, l.khidr@elsevier.com,
Abstract

2:20 61 Cheminformatics career at the Royal Society of Chemistry, UK

Colin Batchelor, batchelorc@rsc.org,
Abstract

2:50 62 Patent law as a non-traditional career in chemistry

Sarah P Hasford, shasford@mcguirewoods.com,
Abstract

3:20   Intermission
3:35 63 Role of personal interests, motivation, and timing in the transitioning to a new career

Svetla Baykoucheva, sbaykouc@umd.edu,
Abstract

4:05 64 From the bench to the board

Rebecca Boudreaux, rebecca@oberonfuels.com,
Abstract

4:35 65 Political "science": Opportunities for chemists in science policy

Ticora V Jones, ticjones@usaid.gov,
Abstract

5:05   Concluding Remarks

Monday, April 8, 2013 8:00 pm - 10:00 pm

Sci-Mix - EVE Session
Morial Convention Center
Room: Hall D
Jeremy Garritano, Organizers
, Presiding
  1 Characterizing the diversity and biological relevance of the MLPCN assay manifold and screening set

Jun Huan, jhuan@ittc.ku.edu,
Abstract

4 PubChem widgets

Lianyi Han, hanl@ncbi.nlm.nih.gov,
Abstract

  6 WITHDRAWN
16 On-line graph mining and visualization of protein-ligand interactome

Clara Ng1, lxi0003@hunter.cuny.edu, Lei Xie1,2, lxi0003@hunter.cuny.edu.
Abstract

17 Encoded Library Technology data analysis: Finding the grain of sand you want without getting a sunburn

Kenneth E Lind, kenneth.e.lind@gsk.com, Neil R Carlson, Ninad V Prabhu, Jeff A Messer.
Abstract

19 How to highlight hits: Advances in visual data analytics tools for HTS data

Jesse A. Gordon, jesse.gordon@dotmatics.com, Jess Sager.
Abstract

26 iBIOMES: Managing and sharing large biomolecular simulation datasets in a distributed environment with iRODS

Julien C Thibault1, julien.thibault@utah.edu, Thomas E Cheatham2,3, Julio C Facelli1,3.
Abstract

28 New cheminformatics microscopes: Combining semantic web technologies, cheminformatical representations, and chemometrics for understanding and predicting chemical and biological properties

Egon L Willighagen, egon.willighagen@maastrichtuniversity.nl,
Abstract

29 Discovery of TLR2 antagonists by virtual screening

Manuela S Murgueitio1, m.murgueitio@fu-berlin.de, Sandra Santos-Sierra2, Gerhard Wolber1.
Abstract

31 On the compound annotation and cleaning the GSK screening collection initiative: The utility of an Inhibition Frequency Index (IFI)

Subhas J Chakravorty, subhas.j.chakravorty@gsk.com, James A Chan, Juan Luengo, Nicole M Greenwood, Ioana Popa-Burke, Ricardo Macarron.
Abstract

32 Analyzing screening and similarity searching outcome in light of multiple approaches to the same target

Tina Garyantes, garyante@optonline.net,
Abstract

  33 WITHDRAWN
36 From hits to leads: Data visualization of chemical scaffolds beyond traditional SAR exploration

Tyler Peryea, tyler.peryea@nih.gov, John Braisted, Ajit Jadhav, Rajarshi Guha, Noel Southall, Dac-Trung Nguyen.
Abstract

41 Reproducible research applied to cheminformatics experiments

Paul J Kowalczyk, paul.kowalczyk@scynexis.com,
Abstract

46 Reverse pharmacognosy: From molecules to active ingredients

Quoc Tuan Do, quoctuan.do@greenpharma.com, Sylvain Blondeau, Philippe Bernard.
Abstract

59 From studying block copolymers to chemical information: A journey of an alternative chemistry career as an academic science librarian

Vincent F Scalfani, vfscalfani@ua.edu,
Abstract

66 From virtual screening to real taste modulators: Bitter blockers and sweetness enhancers

Quoc Tuan Do2, quoctuan.do@greenpharma.com, Terry L. Peppard1, John Scire1, Philippe Bernard2.
Abstract

67 Navigation through chemogenomics data with SPID

Austin B Yongye1, José L Medina-Franco2, jose.medina.franco@gmail.com.
Abstract

68 Inferring odor detection threshold (ODT) using chemical structure based properties

Jae Hong Shin, shin37@indiana.edu, Sebastian E. Ahnert, David J. Wild, Yong-Yeol Ahn.
Abstract

70 ChEMBL tools and services: Creating bridges between cheminformatics and bioinformatics

Mark Davies, mdavies@ebi.ac.uk, Louisa J. Bellis, A. Patricia Bento, Jon Chambers, Anna Gaulton, Anne Hersey, Yvonne Light, George Papadatos, John P. Overington.
Abstract

72 About the impact of open access bioassay data on cheminformatic approaches

Barbara Zdrazil, barbara.zdrazil@univie.ac.at, Gerhard F. Ecker.
Abstract

80 PubChem BioAssay: A public database for chemical biology data

Yanli Wang, ywang@ncbi.nlm.nih.gov,
Abstract

84 Open PHACTS: Meaningful linking of preclinical drug discovery knowledge

Egon L Willighagen1, egon.willighagen@maastrichtuniversity.nl, Christian Brenninkmeijer2, Chris T Evelo1, Lee Harland3, Alasdair J.G. Gray2, Carole Goble2, Andra Waagmeester1, Antony J Williams4.
Abstract

89 Making hidden data discoverable: How to build effective drug discovery engines?

Sebastian Radestock, s.radestock@elsevier.com, Jürgen Swienty-Busch.
Abstract

92 Chemical science that underpins the Reaxys database

Juergen Swienty-Busch1, j.swienty-busch@elsevier.com, Pieder Caduff2, David Evans2.
Abstract

96 Intuitive and integrated browsing of reactions, structures, and citations: The Roche experience

Fausto Agnetti1, Michael Bensch1, Hermann Biller1, Martin Blapp1, Ben Cheikh2, Gerd Blanke1, Joerg Degen1, Bernard Dienon1, Thomas Doerner1, Gunther Doernen1, Frieda Farshchian1, Werner Gotzeina1, Peter Hilty1, Ralf Horstmoeller1, Thomas Jeker1, Brian Jones1, Michael Kappler2, mick.kappler@roche.com, Aslam Momin2, Antonio Regoli1, Denis Ribaud1, Bernard Starck1, Daniel Stoffler1, Klaus Weymann1, Padmanabha Udupa2.
Abstract

101 Withdrawn
109 Novel in silico prediction algorithms for the design of stable and more effective proteins

Francisco G Hernandez-Guzman, francisco.hernandez@accelrys.com, Velin Spassov, Lisa Yan.
Abstract

110 Advanced structural modeling of biologics with BioLuminate

David A Pearlman, Tyler Day, Kathryn Loving, David Rinaldo, Noeris Salam, Dora Warshaviak, Kai Zhu, Woody Sherman, woody.sherman@schrodinger.com.
Abstract

118 Mining frequent itemsets: Constructing topological pharmacophores using pharmacophore feature pairs

Paul J Kowalczyk, paul.kowalczyk@scynexis.com,
Abstract

119 Lexichem: Not another chemical nomenclature app

Edward O Cannon, ed.cannon@eyesopen.com,
Abstract

Tuesday, April 9, 2013 8:15 am - 11:55 am

Linking Bioinformatic Data and Cheminformatic Data - AM Session
Morial Convention Center
Room: 349
Ian Bruno, John Overington, Organizers
Ian Bruno, Presiding
8:15   Introductory Remarks
8:20 69 Integrating chemical and biological structural information

Gary Battle, battle@ebi.ac.uk, Jose Dana, Saqib Mir, Tom Oldfield, Sameer Velankar, Gerard Kleywegt.
Abstract

8:45 70 ChEMBL tools and services: Creating bridges between cheminformatics and bioinformatics

Mark Davies, mdavies@ebi.ac.uk, Louisa J. Bellis, A. Patricia Bento, Jon Chambers, Anna Gaulton, Anne Hersey, Yvonne Light, George Papadatos, John P. Overington.
Abstract

9:10 71 Pharmacological profiling of drugs by linking chemoinformatics and bioinformatics data

Olivier Taboureau, otab@cbs.dtu.dk,
Abstract

9:35 72 About the impact of open access bioassay data on cheminformatic approaches

Barbara Zdrazil, barbara.zdrazil@univie.ac.at, Gerhard F. Ecker.
Abstract

10:00   Intermission
10:15 73 Biological target identification through combination of 3D molecular similarity and lexical similarity of clinical effects

Emmanuel R Yera, ajain@jainlab.org, Ann E Cleves, Ajay N Jain, ajain@jainlab.org.
Abstract

10:40 74 In silico prediction of gene expression profiles for drug-like compounds based on their structural formulae

Alexey Lagunin, alexey.lagunin@ibmc.msk.ru, Sergey Ivanov, Anastassia Rudik, Dmitry Filimonov, Vladimir Poroikov.
Abstract

11:05 75 CAS’ bioactivity and target indicators provide new insights for scientists working at the interface of chemistry and biology

Roger Schenck, rschenck@cas.org,
Abstract

11:30 76 Jikitou biomedical question answering system: Using multiple resources to answer biomedical questions

Michael A. Bauer1,2, mabauer@ualr.edu, Robert E. Belford3, Daniel Berleant1, Roger A. Hall1.
Abstract

Tuesday, April 9, 2013 8:30 am - 11:55 am

Public Databases Serving the Chemistry Community - AM Session
Morial Convention Center
Room: 350
Antony Williams, Sean Ekins, Organizers
Sean Ekins, Presiding
8:30   Introductory Remarks
8:35 77 PubChem: A community driven resource

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

9:05 78 NCI/CADD chemical structure Web services

Markus Sitzmann, sitzmann@helix.nih.gov, Alexey V. Zakharov, Laura Guasch Pàmies, Marc C. Nicklaus.
Abstract

9:35 79 ChemSpider: Disseminating data and enabling an abundance of chemistry platforms

Antony J Williams1, williamsa@rsc.org, Valery Tkachenko1, Ken Karapetyan1, Alexey Pshenichnov1, Dmitry Ivanov1, Colin Batchelor2, Jon Steele2, David Sharpe2.
Abstract

10:05   Intermission
10:20 80 PubChem BioAssay: A public database for chemical biology data

Yanli Wang, ywang@ncbi.nlm.nih.gov,
Abstract

10:50 81 Chemistry-related resources at the Protein Data Bank in Europe

Gary Battle, battle@ebi.ac.uk, Gerard Kleywegt, Sameer Velankar, Tom Oldfield, Swanand Gore, Saqib Mir, Jose Dana.
Abstract

11:20 82 Architecture for an open science molecular compound database

Egon L Willighagen, egon.willighagen@maastrichtuniversity.nl,
Abstract

11:50   Concluding Remarks

Tuesday, April 9, 2013 1:55 pm - 5:30 pm

Linking Bioinformatic Data and Cheminformatic Data - PM Session
Morial Convention Center
Room: 349
Ian Bruno, John Overington, Organizers
John Overington, Presiding
1:55 83 Linking chemical biology information within PubChem

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

2:20 84 Open PHACTS: Meaningful linking of preclinical drug discovery knowledge

Egon L Willighagen1, egon.willighagen@maastrichtuniversity.nl, Christian Brenninkmeijer2, Chris T Evelo1, Lee Harland3, Alasdair J.G. Gray2, Carole Goble2, Andra Waagmeester1, Antony J Williams4.
Abstract

2:45 85 Extracting more value from data silos: Using the semantic web to link chemistry and biology for innovation

Derek Scuffell1, derek.scuffell@syngenta.com, Philip Ashworth2.
Abstract

3:10 86 Roundtripping between small-molecule and biopolymer representations

Noel M O'Boyle1, noel@nextmovesoftware.com, Evan Bolton2, Roger A Sayle1.
Abstract

3:35   Intermission
3:50 87 Representing and registeristing antibody-drug conjugates

Keith T Taylor, keith.taylor@accelrys.com, Burton L Leland, William L Chen, Young-Mi Kwon.
Abstract

4:15 88 Mining chemical and biological data for trends: Visualizing structured numeric data from ELNs

Philip J Skinner, philip.skinner@perkinelmer.com, Phil McHale, Amy Kallmerton, Megean Schoenberg, Anis Khimani, Kate Blanchard, Michael Swartz.
Abstract

4:40 89 Making hidden data discoverable: How to build effective drug discovery engines?

Sebastian Radestock, s.radestock@elsevier.com, Jürgen Swienty-Busch.
Abstract

5:05 90 Applying the law of parsimony in molecular design

Alberto Del Rio, alberto.delrio@gmail.com,
Abstract

Tuesday, April 9, 2013 2:00 pm - 5:25 pm

Public Databases Serving the Chemistry Community - PM Session
Morial Convention Center
Room: 350
Antony Williams, Sean Ekins, Organizers
Antony Williams, Presiding
2:00   Introductory Remarks
2:05 91 Local and remote tracking of molecular dynamics data for global dissemination

Julien C Thibault1, julien.thibault@utah.edu, Thomas E Cheatham2,3, Julio C Facelli1,3.
Abstract

2:35 92 Chemical science that underpins the Reaxys database

Juergen Swienty-Busch1, j.swienty-busch@elsevier.com, Pieder Caduff2, David Evans2.
Abstract

3:05 93 ChemReact: A free database containing more than 524,000 reactions available at your fingertips

Valentina Eigner-Pitto, ve@infochem.de, Hans Kraut, Heinz Saller, Heinz Matuszczyk, Josef Eiblmaier, Peter Loew.
Abstract

3:35   Intermission
3:50 94 Navigating between patents, papers, abstracts, and databases using public sources and tools

Christopher Southan1, Sean Ekins2, ekinssean@yahoo.com.
Abstract

4:20 95 ChemSpider reactions: Delivering a free community resource of chemical syntheses

Valery Tkachenko1, tkachenkov@rsc.org, Colin Batchelor2, Ken Karapetyan1, David Sharpe2, Antony J Williams1.
Abstract

4:50 96 Intuitive and integrated browsing of reactions, structures, and citations: The Roche experience

Fausto Agnetti1, Michael Bensch1, Hermann Biller1, Martin Blapp1, Ben Cheikh2, Gerd Blanke1, Joerg Degen1, Bernard Dienon1, Thomas Doerner1, Gunther Doernen1, Frieda Farshchian1, Werner Gotzeina1, Peter Hilty1, Ralf Horstmoeller1, Thomas Jeker1, Brian Jones1, Michael Kappler2, mick.kappler@roche.com, Aslam Momin2, Antonio Regoli1, Denis Ribaud1, Bernard Starck1, Daniel Stoffler1, Klaus Weymann1, Padmanabha Udupa2.
Abstract

5:20   Concluding Remarks

Wednesday, April 10, 2013 8:30 am - 11:50 am

Balancing Chemistry on the Head of a Pin: Multi-Parameter Optimization - AM Session
Morial Convention Center
Room: 349
Edmund Champness, Matthew Segall, Organizers
Edmund Champness, Matthew Segall, Presiding
8:30   Introductory Remarks
8:35 97 Exploiting a more polar property space in the design of brain penetrant molecules

Anabella Villalobos, anabella.villalobos@pfizer.com, Travis T Wager, Xinjun J Hou, Patrick R Verhoest.
Abstract

9:05 98 Multi-criteria drug discovery: Recent results in building predictive models, combining predictions, and generating new chemistry ideas

Brian B Masek, brian.masek@certara.com, Fabian Boes, Richard Cramer, Roman Dorfman, Stephan Nagy, Lei Wang, Bernd Wendt.
Abstract

9:35 99 Implementation of multi-criteria decision making (MCDM) tools in early drug discovery processes

Marie Ledecq, marie.ledecq@ucb.com,
Abstract

10:05   Intermission
10:20 100 Being suitably sensitive: Balancing competing performance criteria for in silico models

Robert D Clark, bob@simulations-plus.com, Marvin Waldman, Jinhua Zhang, Adam C. Lee, Michael S. Lawless.
Abstract

10:50 101 Withdrawn
11:20 102 Finding multi-parameter rules for successful optimization

Matthew Segall, matt.segall@optibrium.com, Iskander Yusof, Edmund Champness.
Abstract

Wednesday, April 10, 2013 8:30 am - 11:55 am

Public Databases Serving the Chemistry Community - AM Session
Morial Convention Center
Room: 350
Antony Williams, Sean Ekins, Organizers
Antony Williams, Sean Ekins, Presiding
8:30   Introductory Remarks
8:35 103 Universal SMILES: Finally, a canonical SMILES string?

Noel M O'Boyle, baoilleach@gmail.com,
Abstract

9:05 104 Analysis of tautomerism in databases of commercially available compounds

Laura Guasch, lguasch@helix.nih.gov, Markus Sitzmann, Marc C Nicklaus.
Abstract

9:35 105 RSC chemical validation and standardization platform: A potential path to quality-conscious databases

Ken Karapetyan1, karapetyank@rsc.org, Valery Tkachenko1, Colin Batchelor2, David Sharpe2, Antony Williams1.
Abstract

10:05   Intermission
10:20 106 Challenges and recommendations for obtaining chemical structures of industry-provided repurposing candidates

Christopher Southan1, Anthony J Williams2, Sean Ekins3, ekinssean@yahoo.com.
Abstract

10:50 107 One size fits all or how to find the needle in the haystack?

Juergen Swienty-Busch, j.swienty-busch@elsevier.com,
Abstract

11:20 108 Pistoia Alliance AppStore: Apps for life sciences R&D

Alex M Clark, aclark@molmatinf.com,
Abstract

11:50   Concluding Remarks

Wednesday, April 10, 2013 1:30 pm - 3:10 pm

Computational De novo Protein and Peptide Design - PM Session
Morial Convention Center
Room: 349
Cosponsored by COMP
Rachelle Bienstock, Organizers
Rachelle Bienstock, Presiding
1:30   Introductory Remarks
1:45 109 Novel in silico prediction algorithms for the design of stable and more effective proteins

Francisco G Hernandez-Guzman, francisco.hernandez@accelrys.com, Velin Spassov, Lisa Yan.
Abstract

2:10 110 Advanced structural modeling of biologics with BioLuminate

David A Pearlman, Tyler Day, Kathryn Loving, David Rinaldo, Noeris Salam, Dora Warshaviak, Kai Zhu, Woody Sherman, woody.sherman@schrodinger.com.
Abstract

2:35 111 Virtual mutagenesis for optimizing antibody binding affinity: A prospective study

Enrico O. Purisima, enrico.purisima@nrc.ca, Vivcharuk Victor, Traian Sulea, Denis L'Abbé, Yves Durocher, Jason Baardsnes, Maureen O'Connor.
Abstract

3:00   Concluding Remarks

Wednesday, April 10, 2013 1:30 pm - 4:50 pm

Advances in Virtual High-Throughput Screening - PM Session
Morial Convention Center
Room: 350
Joel Freundlich, Sean Ekins, Organizers
Sean Ekins, Presiding
1:30   Introductory Remarks
1:35 112 Setting up a discovery pipeline in KNIME and PipelinePilot: High-throughput de novo design utilizing gigantic virtual chemistry spaces

Carsten Detering, detering@biosolveit.com,
Abstract

2:00 113 New targets addressed by DEKOIS 2.0: Demanding evaluation kits for objective in-silico screening

Frank M. Boeckler, frank.boeckler@uni-tuebingen.de, Matthias R Bauer, Tamer M. I. M. Abdelrehim, Simon M. Vogel.
Abstract

2:25 114 PubChem3D: A virtual screening platform

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

2:50   Intermission
3:05 115 Dual-event machine learning models to accelerate drug discovery

Sean Ekins1,2, ekinssean@yahoo.com, Robert C Reynolds3,4, Hiyun Kim5, Mi-Sun Koo5, Marilyn Ekonomidis5, Meliza Talaue5, Steve Paget5, Lisa Woolhiser6, Anne J Lenaerts6, Barry A Bunin1, Nancy Connell5, Joel S Freundlich5,7.
Abstract

3:30 116 Virtual high-throughput screening of novel pharmacological agents based on PASS predictions

Vladimir V. Poroikov1,2, vladimir.poroikov@ibmc.msk.ru, Dmitry A. Filimonov1, Alexey A. Lagunin1, Tatyana A. Gloriozova1, Olga A. Tarasova1, Pavel V. Pogodin1,2, Marc C. Nicklaus3.
Abstract

3:55 117 How GPUs can find your next hit: Accelerating virtual screening with OpenCL

Simon Krige1, simon@cresset-group.com, Mark Mackey1, Simon McIntosh-Smith2, Richard Sessions2.
Abstract

4:20 118 Mining frequent itemsets: Constructing topological pharmacophores using pharmacophore feature pairs

Paul J Kowalczyk, paul.kowalczyk@scynexis.com,
Abstract

4:45   Concluding Remarks

Thursday, April 11, 2013 8:00 am - 10:45 am

General Papers - AM Session
Morial Convention Center
Room: 349
Jeremy Garritano, Organizers
Jeremy Garritano, Presiding
8:00   Introductory Remarks
8:05 119 Lexichem: Not another chemical nomenclature app

Edward O Cannon, ed.cannon@eyesopen.com,
Abstract

8:30 120 Teach our naming tool to be bilingual: Chinese name-to-structure conversion

David Deng, ddeng@chemaxon.com, Daniel Bonniot.
Abstract

8:55 121 Withdrawn
9:20   Intermission
9:30 122 Withdrawn
 
9:55 123 Withdrawn
10:20 124 Algorithm for efficient conformational equivalence testing without a priori atomic correspondence or connectivity information

Gregory R. Magoon1,2, gmagoon@aerodyne.com, William H. Green2.
Abstract

COMP, Emilio Esposito, Scott Wildman Sunday, April 7, 2013 8:30 am - 11:45 am

Chairs' Prime Choices - AM Session Six Cool Talks #6coolTalks
Morial Convention Center
Room: 357
Cosponsored by BIOL, CINF, MEDI, PHYS, PROF, YCC
Scott Wildman, Organizers
Scott Wildman, Presiding
8:30 1 Computational approach to understanding allostery in human glutathione synthetase
Brandall L. Ingle, Margarita C. De Jesus, Bisesh Shrestha, Mary E. Anderson, Tom R. Cundari.
9:00 2 Mechanisms of stimulation of insulin degrading enzyme (IDE) and substrate specificity of neprilysin (NEP)
Mehmet Ozbil, Rajeev Prabhakar.
9:30 3 Force matching-based force field optimization for thermal conductivity prediction
Yongjin Lee, Gyeong S. Hwang.
10:00   Intermission
10:15 4 Accelerated molecular dynamics on rotatable dihedrals: An efficient statistical sampling technique with improved accuracy
Urmi Doshi, Donald Hamelberg.
10:45 5 Natural atomic orbital representation for optical spectra calculations in the exciton scattering (ES) approach
Hao Li, Vladimir Y Chernyak, Sergei Tretiak.
11:15 6 Highly parallel proton transport simulations on Blue Gene/Q
Adrian W. Lange, Gard Nelson, Christopher Knight, Yuxing Peng, Gregory A. Voth.

COMP, Emilio Esposito, Scott Wildman Monday, April 8, 2013 8:30 am - 11:45 am

Chairs' Prime Choices - AM Session Six More Cool Talks #6coolTalks
Morial Convention Center
Room: 357
Cosponsored by BIOL, CINF, MEDI, PHYS, PROF, YCC
Emilio Esposito, Organizers
Emilio Esposito, Presiding
8:30 69 Role of water bridged hydrogen bonds in ubiquinone binding geometries at the Qi site of cytochrome bc1
Bao-Linh Nguyen, Ralph A Wheeler.
9:00 70 Cluster-enhanced lipid partitioning in membrane domains
Zhenlong Li, Alemayehu A Gorfe.
9:30 71 Molecular dynamics simulations of uranyl-peroxide nanocapsules in aqueous solution
Bess Vlaisavljevich, Pere Miró, Shuxian Hu, Allison Dzubak, Riccardo Spezia, Christopher J. Cramer, Laura Gagliardi.
10:00   Intermission
10:15 72 Computational investigation of the mechanisms for small molecule antagonists of pRb inactivation by HPV-E7
Ara Abramyan, Zhiwei Liu, Vojislava Pophristic.
10:45 73 Developing polarizable potentials for metal-organic materials sorption simulations
Christian R Cioce, Keith McLaughlin, Brant Tudor, Ashley Mullen, Jonathan L Belof, Brian Space.
11:15 74 Exploring residue component contributions to dynamical network models of allostery
Adam T. VanWart, John Eargle, Zaida Luthey-Schulten, Rommie E. Amaro.

COMP, Emilio Esposito, Scott Wildman Wednesday, April 10, 2013 1:30 pm - 5:35 pm

Collaborative Drug Discovery for Neglected Diseases - PM Session
Morial Convention Center
Room: 357
Cosponsored by BIOL, CINF, COMP, MEDI, PHYS, PROF, TOXI, YCC
Johanna Jansen, Rommie Amaro, Wendy Cornell, Y. Jane Tseng, Organizers
Rommie Amaro, Presiding
1:30 397 Judging the ACS Teach-Discover-Treat initiative: Lessons learned and directions for the future
W. Patrick Walters
2:05 398 Structural plasticity of malarial dihydroorotate dehydrogenases demonstrated by X-ray structural analysis of inhibitor bound complexes
Xiaoyi Deng, Farah El Mazouni, Elizabeth J. Goldsmith, Pradipsinh K. Rathod, Margaret A. Phillips.
2:40 399 TDT 2012 Grand Champion: 3D-QSAR-boosted SBVS
Paolo Tosco
3:15   Intermission
3:30 400 Cresset Award: Teaching molecular interactions with online interactive pharmacophore modeling
David R Koes, Carlos J Camacho.
4:05 401 KNIME Award: Computational workflow for human African trypanosomiasis phosphodiesterase inhibitor identification
Khaled M Elokely, Robert J Doerksen.
4:40 402 OpenEye Award: Public domain chemical databases for neglected disease drug discovery
George Nicola, Tiqing Liu, Michael Gilson.
5:15   Panel Discussion

COMP, Emilio Esposito, Scott Wildman Sunday, April 7, 2013 8:30 am - 11:45 am

Computational Study of Water - AM Session #H2O is like OxyClean(R). It Catalyzes in Biological Systems and Materials!
Morial Convention Center
Room: 355
Cosponsored by BIOL, CINF, MEDI, PHYS
Emilio Esposito, Organizers
Seonah Kim, Presiding
8:30 7 Autocatalytic and cooperatively-stabilized dissociative adsorption of water on stepped metal surfaces
Davide Donadio, Rengin Pekoz, Svenja Worner, Luca M Ghiringhelli, Luigi Delle Site.
9:00 8 Role of environment in the catalysis of the MutY DNA repair enzyme
Elizabeth Brunk, Jeremey S Arey, Ursula Rothlisberger.
9:30 9 6N-D water and small molecule distributions from 3D-RISM
Daniel J. Sindhikara, Fumio Hirata.
10:00   Intermission
10:15 10 Predicting the displacement of water molecules from protein hydration sites due to small molecule binding
David J Huggins
10:45 11 Advances in the treatment of water in drug discovery: Applications to affinity and selectivity design
Robert Abel, Goran Krilov, Lingle Wang, Woody Sherman.
11:15 12 Long-range hydrogen-bond structure in aqueous solutions
Richard H Henchman, Sheeba J Irudayam.

 

COMP, Sunday, April 7, 2013 1:30 pm - 4:30 pm

These Materials Rock! @matSci:
Morial Convention Center
Room: 356

 

COMP, Emilio Esposito, Scott Wildman Sunday, April 7, 2013 1:30 pm - 5:15 pm

Computational Study of Water - PM Session #H2O @interfaces == Water at Interfaces.
Morial Convention Center
Room: 355
Cosponsored by BIOL, CINF, MEDI, PHYS
Emilio Esposito, Organizers
Robert Paton, Presiding
1:30 35 WITHDRAWN
2:00 36 Effects of charge transfer on ion adsorption to the liquid water/vapor interface
Marielle Soniat, Steven W. Rick.
2:30 37 Computational studies of aqueous and ionic liquids interfaces
liem dang
3:00   Intermission
3:15 38 Crossing the line: Thermodynamic and structural signatures of methane hydration across the water-vapor interface
Jesse Spencer, Riccardo Baron, Valeria Molinero.
3:45 39 Probing vapor-liquid nucleation of water with advanced simulation method
Troy D Loeffler, Bin Chen.
4:15 40 Modeling vibrational sum-frequency spectra of dicarboxylic acids at the water/air interface
Nicholas A Valley, Geraldine L Richmond.
4:45 41 Water under nanoscopic hydrophobic confinement: Phase behavior, sublimation mechanism, and a novel monolayer ice
Andrew L Ferguson, Nicolas Giovambattista, Peter J Rossky, Athanassios Z Panagiotopoulos, Pablo G Debenedetti.

COMP, Emilio Esposito, Scott Wildman Monday, April 8, 2013 8:30 am - 11:45 am

Computational Study of Water - AM Session Developing a Deeper Understanding of #H2O
Morial Convention Center
Room: 355
Cosponsored by BIOL, CINF, MEDI, PHYS
Emilio Esposito, Organizers
Sami Jaffar, Presiding
8:30 75 Liquid water from first principles: The importance of exact exchange, dispersion interactions, and nuclear quantum effects
Robert A. DiStasio Jr., Biswajit Santra, Zhaofeng Li, Roberto Car.
9:00 am 76 WITHDRAWN
9:30 77 Development of a polarizable water model for solution simulations
Hao Hu
10:00   Intermission
10:15 78 How different is ionic and hydrophobic solvation: DFT vs. point charge models
Marcel D Baer, Christopher J Mundy, Gregory K Schenter.
10:45 79 Approaches for getting benchmark structures and thermodynamics of large water clusters
Berhane Temelso, George C. Shields.
11:15 80 Properties of water and ice from DFT simulations
Joost VandeVondele

COMP, Emilio Esposito, Scott Wildman Sunday, April 7, 2013 8:30 am - 11:45 am

Drug Discovery - AM Session Target-Based: Having the Target in Site for #DrugDisco is More Than Half the Battle #GIjoe
Morial Convention Center
Room: 353
Cosponsored by CINF, MEDI
Scott Wildman, Y. Jane Tseng, Organizers
Zoe Cournia, Presiding
8:30 13 Design of novel TLR antagonists by molecular modeling
Manuela S Murgueitio, Sandra Santos-Sierra, Gerhard Wolber.
9:00 14 Discovery of novel Arp2/3 inhibitors through computer-aided design
George Patargias, Andrew W Baggett, Bradley J Nolen, Zoe Cournia.
9:30 15 Computer-aided Design in Drug Discovery: Featuring case studies of pharmacological targets in prostate cancer
Eleonora Gianti, Randy J Zauhar.
10:00   Intermission
10:15 16 Computational approaches in designing allosteric inhibitors for ITK kinase
Ray J Unwalla, David R Anderson, David C Limburg, Charlie Choi, Mihir D Parikh, Ravi Kurumbail, Ann Aulabaugh, Weidong Ding, Nicole Caspers, Seungil Han, Jeffrey Ohren, Hong Wang, Quintus Medley, Subarna Shakya.
10:45 17 Structural recognition between TWEAK and Fn14: A prelude to discovery of inhibitors for Fn14-TWEAK association
Pooja Narang, Harshil Dhruv, Joseph Loftus, Joachim Petit, Michael Berens, Nhan Tran, Nathalie Meurice.
11:15 18 Hydration entropy from computer simulations
Roland G Huber, Julian E Fuchs, Susanne von Grafenstein, Monika Laner, Hannes G. Wallnöfer, Nemja Abdelkader, Romano T Kroemer, Klaus R Liedl.

COMP, Emilio Esposito, Scott Wildman Sunday, April 7, 2013 1:30 pm - 5:15 pm

Drug Discovery - PM Session Ligand-Based: We Got your Ligands for Ya! #DrugDisco
Morial Convention Center
Room: 353
Cosponsored by BIOL, CINF, MEDI
Scott Wildman, Y. Jane Tseng, Organizers
Caley Allen, Presiding
1:30 42 Whole template CoMFA applies benefits of topomer alignments within the original CoMFA context
Richard D Cramer
2:00 43 Design of new potent inhibitors for the GSK3-beta kinase
N. R. Jena
2:30 44 Application of fragment-based drug design to the discovery of novel anti-HIV microbicides
Olga Tarasova, Dmitry Filimonov, Vladimir Poroikov.
3:00 45 Pharmacophore models of competitive TRPV1 antagonists based on open data
Daria A. Tsareva, Gerhard F. Ecker.
3:30   Intermission
3:45 46 Scaffold hopping for aromatic rings: Can MM compete with QM?
Tim Cheeseright, Mark Mackey.
4:15 47 Conformational and pharmacophoric features within the macrocyclic spiroimine toxins family
Rómulo Aráoz, Jordi Molgó, Bogdan I. Iorga.
4:45 48 Predictive models to better understand the nuances for the oxime-reactivation of cyclosarin, sarin, tabun, and VX inactivated acetylcholinesterase
Emilio Xavier Esposito, Terry R Stouch, Troy Wymore, Jeffry D Madura.

COMP, Emilio Esposito, Scott Wildman Monday, April 8, 2013 8:30 am - 11:45 am

Drug Discovery - AM Session Methodology: Old Problems Require New Solutions. #DrugDisco #answersToYourProblems
Morial Convention Center
Room: 353
Cosponsored by BIOL, CINF, MEDI
Scott Wildman, Y. Jane Tseng, Organizers
Kameron Jorgensen, Presiding
8:30 81 Automated planning of relative free energy calculations
David L Mobley, Shuai Liu, Teng Lin, Yujie Wu, Robert Abel.
9:00 82 Binding site models for affinity prediction guided by protein structure
Rocco Varela, Ajay N Jain.
9:30 83 Enhanced sampling in ligand and polypeptide docking with Glide
Matt Repasky, Jay Banks, Annabhimoju Ramakrishna, Ivan Tubert-Brohman.
10:00   Intermission
10:15 84 Integration of cheminformatics and molecular simulations approaches for accurate prediction of native-like ligand binding poses
Regina Politi, Feng Ding, Nikolay V Dokholyan, Alexander Tropsha.
10:45 85 ProBiS tools: Algorithm, database, and web-server for predicting and modeling of pharmaceutically interesting proteins
Dusanka Janezic
11:15 86 QSAR modeling of imbalanced high-throughput screening data in PubChem
Alexey V Zakharov, Markus Sitzmann, Marc C Nicklaus.

COMP, Emilio Esposito, Scott Wildman Monday, April 8, 2013 1:30 pm - 5:15 pm

Drug Discovery - PM Session Chemical and Structural Informatics: The Most Valuable Commodity I Know of is Information. - Gordon Gekko #informatics #WallStreet
Morial Convention Center
Room: 353
Cosponsored by BIOL, CINF, MEDI
Scott Wildman, Y. Jane Tseng, Organizers
Terry Stouch, Presiding
1:30 110 Measuring complexity and self-similarity of chemical structures in drug discovery
Modest von Korff, Thomas Sander.
2:00 111 Knowledge-based chemical fragment analysis in protein binding sites
Edith Chan, David Selwood, Roman Laskowski.
2:30 112 Return of the tautomers: Toward a global model of tautomerism
Robert Fraczkiewicz, Marvin Waldman, Robert D. Clark, Walter S. Woltosz.
3:00 pm 113 WITHDRAWN
3:30   Intermission
3:45 114 Protein mapping using FTMap with user-defined probe sets
Scott E Mottarella, Dima Kozakov, Sandor Vajda.
4:15 115 Statistical limits of molecular scoring
Gregory A Ross, Garrett M Morris, Philip C Biggin.
4:45 116 Boosting virtual screening enrichments using data fusion: Coalescing 2D fingerprints, shape, and docking
G. Madhavi Sastry, Woody Sherman.

COMP, Emilio Esposito, Scott Wildman Tuesday, April 9, 2013 8:30 am - 11:45 am

Drug Discovery - AM Session ADME/Tox: Designing the Drug is Easy. The Hard Part is Understanding How the Drug Interacts #DrugDisco @acsCOMPprog
Morial Convention Center
Room: 353
Cosponsored by BIOL, CINF, MEDI, TOXI
Scott Wildman, Y. Jane Tseng, Organizers
Kira Armacost, Kira Armacost, Presiding
8:30 151 Bioclipse-OpenTox: Interactive predictive toxicology
Egon Willighagen, Barry Hardy, Nina Jeliazkova, Ola Spjuth.
9:00 152 Development of QSAR models for prediction of hepatotoxicity using post-market data from FDA's AERS database
Xiao Zhu, Barbara L. Minnier, Naomi L. Kruhlak.
9:30 153 Consensus prediction of skin permeability and sensitization using cheminformatics approaches
Eugene Muratov, Vinicius Alves, Denis Fourches, Judy Strickland, Carolina Andrade, Alexander Tropsha.
10:00   Intermission
10:15 154 Accurate calculations of partition coefficients (log POW and log PMW) with atomistic simulation methods
Thorsten Köddermann, Axel W Arnold, Dirk Reith.
10:45 155 Chemistry-Wide Association Studies (CWAS): Determining joint mutagenic effects of co-occurring chemical features
Yen Low, Alexander Sedykh, Denis Fourches, Alexander Golbraikh, Alexander Tropsha.
11:15 156 Progress in predicting pKa of drug-like molecules with ab initio methods
Art D. Bochevarov, Dale A. Braden, Dean M. Philipp, Jeremy R. Greenwood.

COMP, Emilio Esposito, Scott Wildman Tuesday, April 9, 2013 1:30 pm - 5:15 pm

Drug Discovery - PM Session Chemical and Structural Informatics: Information is Power #DrugDisco #informatics
Morial Convention Center
Room: 353
Cosponsored by BIOL, CINF, MEDI, TOXI
Scott Wildman, Y. Jane Tseng, Organizers
Eleonora Gianti, Presiding
1:30 183 Enhancing high throughput screening for Mycobacterium tuberculosis drug discovery using Bayesian models
Sean Ekins, Robert C Reynolds, Baojie Wan, Scott G Franzblau, Joel S Freundlich, Barry A Bunin.
2:00 184 Exact solution to the DNA and protein alignment problem
Milan Randic
2:30 185 Use and abuse of structural data in model validation and analysis
John W Liebeschuetz, Oliver S Smart.
3:00 186 Strategic design of non-covalent interactions in small molecule drug discovery
Rajiah Aldrin Denny
3:30   Intermission
3:45 187 Data are not sufficient: Making the difference in cross-functional project team decisions is the objective
David A. Evans, Juergen Swienty-Busch, Pieder Caduff.
4:15 188 False false positives - problem or red herring?
Mark D Mackey, Timothy J Cheeseright.
4:45 189 Ups and downs of conformer generation: Challenges and solutions derived from structural data
Robin Taylor, Jason C Cole, Oliver Korb, Patrick McCabe.

COMP, Emilio Esposito, Scott Wildman Sunday, April 7, 2013 1:30 pm - 4:45 pm

Material Science - PM Session These Materials Rock! #matSci
Morial Convention Center
Room: 356
Cosponsored by CINF, COLL, PHYS, PMSE, POLY
Maciej Haranczyk, Organizers
Luke Achenie, Presiding
1:30 49 Efficient and precise techniques for parallel kinetic Monte Carlo simulations
Jerome P Nilmeier
2:00 50 Withdrawn
2:30 51 Computational study of the stability and diameter dependence of poly-carbazole wrapped single-walled carbon nanotubes
Michael L Mayo, David Hogle, Svetlana V Kilina.
3:00   Intermission
3:15 pm 52 WITHDRAWN
3:45 53 Quantitative structural solution of rare earth doped disordered up-conversion material β-NaLaF4
Tara M Michels-Clark, Michal Chodkiewicz, Robert J Harrison, Christina Hoffmann, Jürg Hauser, Anthony Linden, Vickie Lynch, Thomas Weber, Hans-Beat Bürgi.
4:15 54 Effect of capping ligands on optical properties of PbSe quantum dots
Mary Margaret Hedrick, Svetlana V Kilina.

COMP, Emilio Esposito, Scott Wildman Monday, April 8, 2013 1:30 pm - 5:20 pm

Material Science - PM Session More Material Madness #matSci
Morial Convention Center
Room: 356
Cosponsored by CINF, COLL, PHYS, PMSE, POLY
Maciej Haranczyk, Organizers
Cheng-Tsung Lai, Presiding
1:30   Introductory Remarks
1:35 117 Surface modified TiO2 photocatalysts: Insights from first principles simulations
Anna Iwaszuk, Michael Nolan.
2:05 118 Surface reactivity/stability and hydration of calcium silicate phases
Can Ataca, Engin Durgun, Hamlin H. Jennings, Jeffrey C. Grossman.
2:35 119 Computational investigation of reactions at metal/water interfaces
Muhammad Faheem, Andreas Heyden.
3:05 120 Building a chemical intuition under pressure: Prediction of polyhydride and subhydride phases
Eva Zurek
3:35   Intermission
3:50 121 Computational study on the proton affinity and thermophysical properties of imidazole derivatives
Haining Liu, Jason E Bara, C. Heath Turner.
4:20 122 Computational screening of mixed metal halide ammines
Peter Bjerre Jensen, Steen Lysgaard, Ulrich Quaade, Tejs Vegge.
4:50 123 Crystallization of ionic lipid membranes, elucidated by atomistic simulation
Baofu Qiao, Monica Olvera de la Cruz.

COMP, Emilio Esposito, Scott Wildman Tuesday, April 9, 2013 1:30 pm - 5:15 pm

Membranes - PM Session Inner Leaflet #InsaneInTheMembrane #throwback
Morial Convention Center
Room: 356
Cosponsored by BIOL, CINF, COLL, PHYS
Michael Feig, Organizers
Amber Carr, Presiding
1:30 190 Probing the deprotonation mechanism of the His37 tetrad in the M2 channel from the influenza A virus via molecular simulation
Hao Dong, Michael L Klein, Giacomo Fiorin.
2:00 191 Molecular dynamics study of the Cytolysin A pore forming toxin using atomistic and coarse grained simulations
Swarna M Patra, Rajat Desikan, Prabal K Maiti, Ganapathy Ayappa.
2:30 192 Ras dynamics, membrane binding, and assembly
Alemayehu A Gorfe, Zhenlong Li, Hualin Li.
3:00 193 Molecular dynamics and enhanced sampling simulations of a membrane-bound reaction center protein
David N LeBard
3:30   Intermission
3:45 194 Probing the Meta I to Meta II equilibrium of rhodopsin activation in detergent micelles with molecular dynamics simulations
Blake Mertz, Michael F Brown, Edward Lyman.
4:15 195 What can we learn from microsecond simulations of a peripheral membrane protein of yeast?
Brent Rogaski, Jeffery B. Klauda.
4:45 196 Fatty acid amide hydrolase (FAAH) substrate specificity understood via molecular dynamics
Giulia Palermo, Pablo Campomanes, Marilisa Neri, Daniele Piomelli, Andrea Cavalli, Ursula Rothlisberger, Marco De Vivo.

COMP, Emilio Esposito, Scott Wildman Wednesday, April 10, 2013 1:30 pm - 4:45 pm

Membranes - PM Session Outer Leaflet #membraneInsanity #outerSpace
Morial Convention Center
Room: 356
Cosponsored by BIOL, CINF, COLL, PHYS
Michael Feig, Organizers
Adam VanWart, Presiding
1:30 418 Coarse-grained molecular dynamics of PEGylated assemblies
Sharon M. Loverde, Wataru Shinoda, Dennis E. Discher, Michael L. Klein.
2:00 419 Nanoparticle-membrane interactions: Insights from coarse-grained MD simulations
Paraskevi Gkeka, Panagiotis Angelikopoulos, Zoe Cournia.
2:30 420 Oxygen diffusion in water, alkanes, and lipid bilayers
An Ghysels, Richard M Venable, Richard W Pastor, Gerhard Hummer.
3:00   Intermission
3:15 421 Lipid 12: Accurate membrane simulations with a redesigned modular phospholipid force field for AMBER
Ross C Walker, Benjamin Madej, Ian R Gould, Callum J Dickson.
3:45 422 Dissecting lipid–protein interaction in ABC transporters
Ronald D. Hills, Jr
4:15 423 Withdrawn

COMP, Emilio Esposito, Scott Wildman Wednesday, April 10, 2013 8:30 am - 11:45 am

Mobile Applications - AM Session Can you Calculate Me Now? (Tweet Along with Us! Use #compMobile)
Morial Convention Center
Room: 357
Cosponsored by CINF, MEDI
Scott Wildman, Organizers
Scott Wildman, Presiding
8:30 367 TB Mobile: Appifying data on antituberculosis molecule targets
Sean Ekins, Alex M Clark, Malabika Sarker, Carolyn Talcott, Barry A Bunin.
9:00 368 Mobile + Cloud: A replacement for desktop cheminformatics?
Alex M Clark
9:30 369 Molecular modeling on iOS devices
Warren Hehre
10:00   Intermission
10:15 370 Expanding the reach of cheminformatics through mobile computing
Steven M Muskal
10:45 371 iMolview: A multiplatform mobile application for biologists and chemists
Maxim Totrov, Eugene Raush, Ruben Abagyan.
11:15 372 Facilitating collaborative molecular visualization using mobile PyMOL
Jason Vertrees

COMP, Emilio Esposito, Scott Wildman Wednesday, April 10, 2013 1:30 pm - 5:25 pm

Nanosimulations and Nanoinformatics - PM Session Big Talks About Little Things #nanoInfo #nanoSims
Morial Convention Center
Room: 351
Cosponsored by BIOL, CINF, MEDI, TOXI
Alexander Tropsha, Organizers
Alexander Tropsha, Presiding
1:30   Introductory Remarks
1:35 431 Inorganic nanographenes: Innovations by computations
Zhongfang Chen
2:05 432 Computational nanotoxicology: Nano-QSARs, protein-ligand docking, and quantum-chemical methods for toxicity prediction of nanoparticles
Bakhtiyor Rasulev, Danuta Leszczynska, Jerzy Leszczynski.
2:35 433 Impact of biological endpoints on the descriptor pool: Using decorated nanotubes to understand the role of spatial descriptors
Chi-Yu Shao, Sing-Zuo Chen, Bo-Han Su, Yufeng J Tseng, Emilio Xavier Esposito, Anton J Hopfinger.
3:05 434 Exploring mechanistic inference of decorated nanotubes using multiple descriptor classes
Yufeng J Tseng, Chi-Yu Shao, Sing-Zuo Chen, Bo-Han Su, Emilio Xavier Esposito, Anton J Hopfinger.
3:35   Intermission
3:50 435 Adsortion and oxidation of ethanol on Pt-particles supported by defective graphene
Yixuan Wang, Zhenfeng Xu.
4:20 436 From metal to molecules: Probing the limits of melting in small gallium clusters
Nicola Gaston, Krista G. Steenbergen.
4:50 437 Simulating “soft” electronics
Timothy Clark
5:20   Concluding Remarks

COMP, Emilio Esposito, Scott Wildman Tuesday, April 9, 2013 6:00 pm - 8:00 pm

Poster Session - EVE Session
Morial Convention Center
Room: Hall A, Sec D
Cosponsored by ANYL, CHED, CINF, COLL, MEDI, ORGN, PHYS, PMSE, POLY
Emilio Esposito, Organizers
, Presiding
  219 Chemical bonding in graphene, its derivatives, and several polycyclic aromatic hydrocarbons
Alexander I Boldyrev, Ivan A Popov.
  220 Hydration free energy calculations show that amino acid hydrophobicity is strongly environment-dependent
Kimberly S Keyes, Pavel V Klimovich, David L Mobley.
  221 MP2 and DFT study of the selectivity of NADP binding sites for novel ligands
Rachel K Sanders, Mauricio Cafiero.
  222 MP2 and DFT calculations of interactions of boronated and non-boronated intercalants in small nucleic acid models
Ashley Tufton, Mauricio Cafiero.
  223 Application of alchemical binding free energy calculations and other computational methods to aid the discovery of antibacterial drugs
Vivian Jaber
  224 MP2 and DFT analysis of the ligand selectivity of two sulfotransferase enzymes
Diana Bigler, Hallie Weems, Mauricio Cafiero.
  225 Acceleration of quantum chemistry and chemical similarity calculations on GPGPU architecture toward faster virtual screening
Ryota Koga, Yuki Furukawa, Koji Yasuda, Naoki Nariai.
  226 Binding energies of electron-rich and electron-deficient stacked arene-arene complexes: Substituent effects and SAPT analysis
Laura K Hardebeck, Michelle Watt, Charles C Kirkpatrick, Michael Lewis.
  227 Computer simulations of crystallization of the ionic liquid [dmim+][Cl-] in the bulk
Xiaoxia He, Francisco R Hung, Erik E Santiso.
  228 CrystalDock: Leveraging known structural information for fragment-based drug design
Aaron J Friedman, Jacob D Durrant, James A McCammon.
  229 Ab initio electronic structure program Jaguar: New in version 8.0
Art D. Bochevarov
  230 Molecular dynamics simulation of the interaction between cholates and cholesterol
Madeline Reed
  231 How molecular interactions between terpenoid mosquito repellents and attractants may affect repellency?
Shengliang Liao, Zongde Wang, Jie Song, Guorong Fan, Shangxin Chen, Peng Wang, Jinzhu Chen.
  232 Estimating activation free energy for hydration of perfluoroaldehyde and glyoxal
Osamu Setokuchi
  233 Q-Chem 4.1: The latest advances in methods and algorithms in the Q-Chem program package
Zhengting Gan, Evgeny Epifanovskiy, Emil Proynov, Yihan Shao.
  234 Computational studies of the molecular mechanisms responsible for Ca2+ permeation and Mg2+ block of NMDA receptors
Lea Veras, Igor Kurnikov, Jon W Johnson, Maria Kurnikova.
  235 Application of fast Fourier transforms on frequency-modulated continuous-wave radars
Dwayne M Brooks, Jamiiru Luttam Luttamaguzi, Akbar Eslami.
  236 Exploration of mechanism between nanotoxicity and protein targets: QSAR models using nanotoxicity endpoints of decorated nanotubes
Chi-Yu Shao, Sin-Zuo Chen, Bo-Han Su.
  237 New approach of traditional Chinese medicine taxonomy: Using marker ingredients as bases
Kuo-Hsiang Hsu, Yufeng J. Tseng.
  238 Development of OPLS-AA force field parameters for ionic liquid simulations and their applications in elimination reactions
Somisetti V Sambasivarao, Caley Allen, Orlando Acevedo.
  239 Multi-ligand docking in the minor groove of DNA
Chrystal D Bruce, Maddi Ferrara.
  240 Molecular modeling of the ionic liquid [EMIM+][TFMSI-] confined in model nanoporous materials
Nav N Rajput, Joshua Monk, Ramesh Singh, Francisco R Hung.
  241 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.
  242 C-H activation of cycloalkanes with the Cp'Rh(CO) fragment: A computational study
Amanda L Renz, Michael B. Hall.
  243 Structural modeling of the relaxin peptide receptor and its small molecule agonists
Xin Hu, Zaohua Huang, Noel Southall, Jingbo Xiao, Catherine Z. Chen, Elena Barnaeva, Juan J. Marugan, Marc Ferrer, Wei Zheng, Irina U. Agoulnik, Alexander I. Agoulnik.
  244 Elucidation of the molecular interactions between neuraminidase and sialic acid
Alvin R Wu, Leah Krause, Adam Van Wynsberghe.
  245 Computational investigation of the interactions of lysyl oxidase with its natural substrates
Michael Lynch, Daniel Turman, Faina Ryvkin.
  246 Investigation of the effects of electronic desolvation on oseltamivir binding kinetics to N1 influenza neuraminidase
Carmen M Montagnon, Robert B Clayton, Adam W. Van Wynsberghe.
  247 Exploring ionic liquid induced mechanistic changes for β-elimination reactions from QM/MM simulations
Caley R Allen, Somisetti V Sambasivarao, Orlando Acevedo.
  248 QM/MM simulations for the elucidation of ionic liquid effects upon classical organic reactions
Caley R Allen, Orlando Acevedo.
  249 Energetic and structural basis for DNA damage recognition by human 8-oxoguanine glycosylase
Haoquan Li, Dmitry O Zharkov, Carlos de Los Santos, Arthur P Grollman, Carlos Simmerling.
  250 Computational approach to the prediction of enzyme specificities
David B Williams-Young, Jaeju Ko, Mary Jo Ondrechen.
  251 BindingDB: A protein-ligand database for drug discovery
George Nicola, Tiqing Liu, Linda Hwang, Michael Gilson.
  252 Classification tree and random forest based prediction models on molecular autofluorescence
Yi-Shu Tu, Tze-Hao Lin, Yufeng J Tseng.
  253 Heat of formation of ethenone
Kevin Range, Julia Tiaw.
  254 Quantum mechanical studies of thiohydroxycarbene
Jean M. Standard
  255 Investigating substrate-induced conformational changes in alkanesulfonate monooxygenase using molecular dynamics simulations
Kira A Armacost, Symon Gathiaka, Holly Ellis, Orlando Acevedo.
  256 Computing relative acidities of phenol derivatives in DMSO and water with isodesmic equations
Katherine L. Munroe, David H. Magers.
  257 Relative acidities of barbituric acid and thiobarbituric acid
Jonathan E. Landrum, Katherine L. Munroe, David H. Magers.
  258 Computational studies of isomers of C80
Taylor McKee, J. Paige Buchanan, David H. Magers.
  259 Relative stabilities of derivatives of 6-methylpentacene and 6-methylene-6,13-dihydropentacene
Marika Zarafyan, Bei Cao, David H. Magers.
  260 Characterization of excited states via FFT time-correlation functions: IR spectrum for conjugated molecules
Johan F Galindo Cruz, Sebastian Fernandez-Alberti, Adrian E Roitberg.
  261 Calculating enthalpies of formation for the oxadiazoles and their cyano derivatives via isodesmic and homodesmotic reactions
Shelby L. Raines, Sarah E. DeLee, Erica Q. Chong, Glake Hill, David H. Magers.
  262 Determining the protonation state of the active site residues of Laminaripentaose-producing β-1,3-glucanase
Shuhua Ma, Xiaochen Zhang.
  263 Conventional strain energies of the diazetidines and the diphosphetanes
Shelley A. Smith, Ashley R. McDonald, Patricia H. Stewart, Glake Hill, David H. Magers.
  264 Computational insight to molecular imprinting
Julia M Saloni
  265 Computational analysis of the electrostatic interaction between chronic myeloid leukemia drugs and Bcr-Abl kinase
Lucy Y Liu, Mala L Radhakrishnan.
  266 Extension of Redfield theory: Inclusion of non-elastic collisions
Shin-ichiro Sato
  267 Virtual screening for new γ-aminobutyric acid transporter 1 inhibitors based on insights acquired by comparative modeling
Andreas Jurik, Barbara Zdrazil, Harald H Sitte, Gerhard F Ecker.
  268 Estimating protein-protein electrostatic binding energetics: A feature-based approach
Amelia B Kreienkamp, Mala L Radhakrishnan, Finale Doshi-Velez.
  269 Comparison of resonance-assisted hydrogen bonding in carboxyphosphate and structural analogs
Sebastien Hebert, Venkata Pakkala, Steven Firestine, Jeffrey Evanseck.
  270 Molecular dynamics simulations of bacterial interaction with hydrophilic surfaces
Divesh Bhatt
  271 Effects of ethanol on the toll-like receptor 3 - RNA complex: A molecular dynamics study
Chinthaka N Ratnaweera, Steven R Gwaltney.
  272 Development and implementation of multilevel Generalized Distributed Data Interface in GAMESS
Alexander Gaenko, Ryan Olson, Mark S Gordon.
  273 LMRSDCI method in GAMESS: Localization, parallelization, and performance analysis
Alexander Gaenko, David Krisiloff, Mark S Gordon, Emily A Carter.
  274 Influenza fusion peptides prime lipids for membrane fusion using specific interactions
Sébastien Légaré, Patrick Lagüe.
  275 Assessment of correction methods for intramolecular basis set superposition error
xavier barbeau, Patrick Lagüe.
  276 Analysis of chemical networks: A novel paradigm for optimal synthesis
Chris M Gothard, Nosheen A Gothard, Bartosz A Grzybowski.
  277 Effects of lipid binding on the structure of human paraoxanase1
Steven Gwaltney, Manikanthan Bhavaraju.
  278 C-O bond cleavage using transition metal catalysts: From dimethyl ether activation to lignin degradation
Cong Liu, Angela K Wilson.
  279 Calculation of redox potentials of type-I blue copper proteins using quantum mechanical/molecular mechanical simulations
Thomas G. Bartholow, Sudeep Bhattacharyya, Sudeep Bhattacharyya.
  280 Versatility of chloroperoxidase catalytic function: Apoenzyme tunes reactivity of the active center
Alexander N. Morozov, Armando D. Pardillo, David C. Chatfield.
  281 Disulfide bond in human neuroglobin determines heme-apoenzyme hydrogen bonding: A possible mechanism for redox control of neuroprotective activity
David C. Chatfield, Alexander N. Morozov, James P. Roach.
  282 Simultaneous loop prediction for homology modeling
Steven V Jerome, Richard A Friesner.
  283 Quantum chemical studies of the binding and catalytic hydride transfer reaction of flavin with aromatic substrates
Caitlin Bresnahan, Yer Yang, Sudeep Bhattacharyya.
  284 Information-driven fully flexible HADDOCKing: Performance on a benchmark of protein-ligand complexes
Jeffrey S Grinstead, Tracy L Wormwood, Aurelien Thureau, Rolf Boelens, Alexandre M.J.J. Bonvin.
  285 Withdrawn
  286 Withdrawn
  287 Quantum chemical studies on the mechanism and selectivity of indole direct arylations
Sami K Jaffar, Simone Tomasi, Robert S Paton.
  288 Halogen bonding in rational drug design: Targeting histidine
Andreas Lange, Markus O Zimmermann, Rainer Wilcken, Frank M Boeckler.
  289 Organocatalysts for biorenewable desymmetrization
Milan Cvitkovic, David Alberg, Gretchen Hofmeister, Daniela Kohen.
  290 Insights into the long-time dynamics, structural properties, and thermalstabilities of serine hydrolase enzymes from molecular dynamics and normal mode analysis
Habib U Rehman, Steven R Gwaltney.
  291 Theoretical study of the electronic structure of gold clusters over graphene
Alan Miralrio, Luis E Sansores.
  292 Rational modulation of enzyme-inhibitor residence time for the mycobacterium tuberculosisenoyl-ACP reductase InhA
Cheng-Tsung Lai, Pan Pan, Nina Liu, Weixuan Yu, Lauren Spagnuolo, Sonam Shah, Gopal R. Bommineni, Peter Tonge, Carlos Simmerling.
  293 Conformational and structural dynamics of K-ras and H-ras proteins: Specificity at the catalytic domain?
Nandini Rambahal, Harrison H. Hocker, Alemayehu A. Gorfe.
  294 Modeling of potent and selective kappa opioid receptor peptide inhibitors in light of the X-ray crystal structure
Karina Martinez-Mayorga, Kendal G. Byler, Austin B. Yongye, Marc A. Giulianotti, Colette T. Dooley, Richard A. Houghten.
  295 Molecular modeling of trypanosomal cathepsins
Karina Martinez-Mayorga, Kendall G. Byler.
  296 Polarizable force field OPLS-AAP applied to proteins and carbon surfaces
Patric Schyman, William L. Jorgensen.
  297 Novel approach to detect and visualize aggregation-prone residues in immunoglobulins
Elizabeth Sourial
  298 Rationalization and visualization of non-bonded interactions using extended Hückel theory
Alain Ajamian
  299 Computational docking of pyrazole derivatives into CYP2E1
Joseph W. Levy, Grover P. Miller, Martin D. Perry, Jr..
  300 Theoretical investigation of the reactivity of Ir(II) sulfides, Ir2(μ-S)2(PPh3)4 and Ir2(μ-S)2(PH3)4
Stella Kritikou, Michael B. Hall.
  301 Organic solvent-induced conformational transition of an amphiphilic peptide
Quentin R. Johnson, Ricky Nellas, Tongye Shen.
  302 Bringing clarity to the prediction of protein-ligand binding free energies via blurring
Melek N. Ucisik, Zheng Zheng, John C. Faver, Kenneth M. Merz Jr..
  303 Molecular dynamics investigation of CD44 hyaluronan binding domain with sialic acid-terminal N-glycans
Christina E. Faller, Olgun Guvench.
  304 Exploring the conformational landscape of decaprenyl pyrophosphate synthase, a promising drug target against tuberculosis
Meekyum O Kim, William Sinko, César de Oliveira, Eric Oldfield, J. Andrew McCammon.
  305 Oxygen diffusion pathways in a cofactor-independent oxygenase
Natali V Di Russo, Heather L Condurso, Steven D Bruner, Adrian E Roitberg.
  306 Linear relationship between computed energies and pKa for carboxylic acids and amides
Obsa L Bokku, Melissa C Denler, Joseph D Alia.
  307 Natural bond orbitals related to the pKa of carboxyl acids and phenols
Abdala Bashir, Tiwaloluwa Ajibewa, Finhas Ogbazghi, Joseph D Alia.
  308 Structural models for the interaction of pentamidine analogs with the NMDA receptor
Madhusoodanan Mottamal, Michael L Berger, Jean Jacques Vanden Eynde, Dorota Maciejewska, Ivana Jarak, Tien L Huang.
  309 Aggregation-volume-bias Monte Carlo investigation of vapor-liquid nucleation at varying dimensionalities: A comparison to classical nucleation theory
Andrew Galtas, Troy D Loeffler, Bin Chen.
  310 Comparison of coarse-grained and atomistic-level simulations for aminoacyl tRNA-synthetases
Alexander M Strom, Sudeep Bhattacharyya, Sanchita Hati.
  311 Automated docking receptor selection workflow for non-nucleoside reverse transcriptase drug discovery
Richard A Stanton, Kyle A Brown, Karan Uppal, Kim M Gernert, James H Nettles, Raymond F Schinazi.
  312 Withdrawn
  313 Force field development for thiolated gold nanoclusters
Maegan N Dailey, Sandipan Banerjee, Jose A Gascon.
  314 Leveraging structural knowledge gained from accelerated molecular dynamics simulations of IspG and IspH to inform development of novel inhibitors of the non-mevalonate pathway
Patrick G Blachly, César de Oliveira, J. Andrew McCammon.
  315 Withdrawn
  316 Towards the identification of small molecule Ras inhibitors: A dynamics-guided approach
Harrison Hocker, Nandini Rambahal, Alemayehu Gorfe.
  317 Comparing post Hartree-Fock models with DFT for the gas-phase dissociation of branched aminonitile moieties
William D Price, Hannah E Bott, Charles Doerner, Kristina Gemayel.
  318 Theoretical modeling of silicon halides
David G Hogle, Svetlana V Kilina.
  319 Graphene oxide together with carbon nanotubes: A computational study
Daniel B Lawson
  320 Iron (ii) complex spin crossover characteristics
Heather Leask, Pascal Lacroix, Pascal Lacroix, Jose-Antonio Real.
  321 Molecular dynamics of the Hsp70 chaperone's Nucleotide Binding Domain: Understanding nucleotide binding and structure-function relationships
Ewa I Golas, Cezary Czaplewski, Adam Liwo, Harold A Scheraga.
  322 Calculated pKa values for amino acid side chains near the ubiquinone and ubiquinol binding sites of cytochrome bc1
Ralph A Wheeler, Bao-Linh Nguyen.
  323 Unraveling the twist: Designing Mobius twist molecules
Christopher V Donnay, Sharaai Marrero, Camilla Montonen, Michelle M Francl.
  324 Simulation studies of ether-alkane mixtures adsorbed on solid substrates
James Lee, Selena R. Watkins, Kelly E. Anderson, J. Ilja Siepmann.
  325 Electronic effects of Zn(II)tetrakis(phenyl)porphyrin encapsulation into a Zn(II) carboxylate MOF, USF1
Christi L Whittington, Randy W Larsen, H Lee Woodcock.
  326 Theoretical comparison of C-H activation rates of CpRh(R); R=CO or CNCH3
Joana E Cisneros, Amanda Renz, Michael Hall.
  327 Validation of a tuned interfacial parameter set using dual-force-field CHARMM for the accurate simulation of protein adsorption on a silica glass surface
James Snyder, Tigran Abramyan, Jeremy A Yancey, Steven J Stuart, Robert A Latour.
  328 Do androids dream of electronic documents?
Ron Massicotte
  329 Improved nucleic acid descriptors for siRNA efficacy prediction
Simone Sciabola, Robert Stanton, Qing Cao, Ignacio Faustino, Modesto Orozco.
  330 DNA damage induced by electrophilic alkylating agents generated from nitrosoureas: A theoretical investigation of mechanism and structure-carcinogenicity relationship
Lijiao Zhao, Rugang Zhong, Tingting Liu.
  331 Ras conformational dynamics: Novel-reaction coordinates and role of conserved waters
Priyanka Prakash, Abdallah Sayyed-Ahmad, Alemayehu A Gorfe.
  332 Potential surface editing to accelerate conformational searching
Joseph T Allison, Anthony K Rappé.
  333 Fast and accurate prediction of drug binding affinity by similarity-based docking and machine learning
Michal Brylinski
  334 Solid state adaptive natural density partitioning: A tool for deciphering chemical bonding in periodic systems
Timur R. Galeev, Benjamin D. Dunnington, J. R. Schmidt, Alexander I. Boldyrev.
  335 Acceleration of high-throughput molecular docking for novel drug discovery on supercomputers
Sally R Ellingson, Jeremy C Smith, Jerome Baudry.
  336 Structural assessment for active and selective kinase inhibitors: GSK-3β and CDK2 case studies
Khaled M Elokely, Gang Fu, Robert J Doerksen.
  337 Dynamical network models of allostery for hisH-hisF without alpha-carbons
Adam T. VanWart, John Eargle, Zaida Luthey-Schulten, Rommie E. Amaro.
  338 Characterization of the wide-open flap state of Klebsiella
Abstract
  339 WITHDRAWN
  340 Vibronic switching of fluorescence output from urea-functionalized poly (p-phenylene) receptor by fluoride-anion recognition
Yanai Kazuma, Shimada Ryotaro, Fuchise Keita, Kakuchi Ryohei, Sakai Ryosuke, Satoh Toshifumi, Kakuchi Toyoji, Sato Shin-ichiro.
  341 WITHDRAWN
  342 Novel method for computer-based entropy estimation: Application to model molecular processes
James Robertson, Victor Holanda Rusu, Riccardo Baron.
  343 Characterizing and exploiting the properties of water in protein active sites for rational drug design and discovery
Tom Kurtzman Young
  344 Novel coarse-grained force field for carbohydrates
Victor H Rusu, Riccardo Baron, Roberto D Lins.
  345 Cross-docking to identify antibody-antigen interaction partners
Krishna Praneeth Kilambi, Jeffrey J Gray.
  346 Structurally aligned local sites of activity (SALSAs) computational method for the prediction of function of structural genomics proteins
Joslynn S Lee, Mary Jo Ondrechen.
  347 Time-dependent density functional theory-based modeling of functionalization of cyclohexasilane and related compounds
David G Hogle, Svetlana V Kilina.
  348 WITHDRAWN
  349 Assessing the applicability of pairwise alternatives to Ewald summation on a wide range of ionic liquids
Billy Wayne McCann, Orlando Acevedo.
  350 Modular amber lipid force field for the simulation of complex membranes and membrane bound proteins
Benjamin D Madej, Callum J. Dickson, Ross C Walker, Ian R. Gould.
  351 Off-Path simulation method: A new chain-of-replica approach for sampling reaction processes
Justin K White, Milan Hodoscek, Henry L Woodcock.
  352 Computational study of the selective dispersing of single-walled carbon nanotubes by ssDNA
Chantel I. Nicolas
  353 Solvent effects and dynamic averaging of 195Pt NMR shielding in cisplatin derivatives using ab inito molecular dynamics (MD) and DFT
Kiplangat Sutter, Jochen Autschbach, Lionel Truflandier.
  354 Ensemble molecular dynamics approach to characterizing the protein-ligand complex: Residual inhibitor entropy enhances drug potency
Amethyst Radcliffe, Benjamin Pham, Samantha Cao, Phuc La, Eric Sorin, Richard Wang, Yi An.
  355 Diagrammatic vibrational structure methods for molecules and solids
Matthew R Hermes, Murat Keçeli, So Hirata.
  356 Withdrawn
  357 Quantitative structure-activity relationships (QSAR) for oral chemical health guidance values
Yunfeng Tie, G. Sarah Sirin, James S. Holler, Eugene Demchuk.
  358 Withdrawn
  359 Crystallographic waters: To displace or not to displace?
Alexander S. Bayden, Demetri T. Moustakas, Diane Joseph-McCarthy, Michelle L. Lamb.
  360 RNA/peptide binding driven by electrostatics: Insights from bi-directional pulling simulations
Trang N Do, Paolo Carloni, Gabriele Varani, Giovanni Bussi.
  361 WITHDRAWN
  362 Global optimization techniques utilized to generate new accurate VLE force fields for ethylene oxide as a test case
Andreas Krämer, Marco Hülsmann, Jadran Vrabec, Dirk Reith.
  363 Using compendia as a collaborative tool in neglected diseases drug discovery
Paul J Kowalczyk
  364 Free energetics of polyarginine peptides in model lipid bilayers via molecular dynamics simulations
Sandeep Patel, Yuan Hu.
  365 Molecular dynamics study of spanning networks of protein hydration water
Sandeep Patel, Di Cui.
  366 Withdrawn

COMP, Emilio Esposito, Scott Wildman Monday, April 8, 2013 9:00 am - 11:45 am

Potential Function Uncertainty and Validation - AM Session Potential Model Development
Morial Convention Center
Room: 356
Cosponsored by BIOL, CINF, MEDI, PHYS
John Faver, Kenneth Merz, Organizers
John Faver, Kenneth Merz, Presiding
9:00 87 Toward a comprehensive polarizable macromolecular force field based on the CHARMM classical drude oscillator model
Alexander D. MacKerell Jr.
9:30 88 Accurate and efficient quantum chemical methods for structures and non-covalent interactions in large bio- and supra-molecular systems
Stefan Grimme
10:00 89 Polarizable atomic multipole-based AMOEBA force field for proteins
Pengyu Ren
10:30   Intermission
10:45 90 Developing force fields to run on specialized hardware
John L Klepeis, David E Shaw.
11:15 91 Force-field development for computer simulation of biomolecular systems: The GROMOS case
Wilfred F. van Gunsteren

COMP, Emilio Esposito, Scott Wildman Tuesday, April 9, 2013 9:00 am - 11:45 am

Potential Function Uncertainty and Validation - AM Session Predictions and Benchmarking
Morial Convention Center
Room: 356
Cosponsored by BIOL, CINF, MEDI, PHYS
John Faver, Kenneth Merz, Organizers
John Faver, Kenneth Merz, Presiding
9:00 157 Next generation of benchmarks for non-covalent interactions, and challenges from charge penetration effects
C. David Sherrill
9:30 158 Development of new density functionals and their validation against broad databases
Roberto Peverati, Donald G. Truhlar.
10:00 159 Prediction of structure and binding affinity of protein-protein complexes
Alexandre M.J.J. Bonvin
10:30   Intermission
10:45 160 Prediction of binding affinities with a Poisson-Boltzmann continuum solvent model
Junmei Wang
11:15 161 Can we predict what is predictable? UsingMarkov State Models to elucidate robustness of potentials in molecular simulation
Vijay S. Pande

COMP, Emilio Esposito, Scott Wildman Wednesday, April 10, 2013 9:00 am - 11:00 am

Potential Function Uncertainty and Validation - AM Session Predictions and Benchmarking
Morial Convention Center
Room: 356
Cosponsored by BIOL, CINF, MEDI, PHYS
John Faver, Kenneth Merz, Organizers
John Faver, Kenneth Merz, Presiding
9:00 386 Next generation of databases for benchmark binding energies
Kevin E. Riley
9:30 387 Binding assays by computer simulations: Capabilities, accuracy, and precision
Gianni D De Fabritiis
10:00 388 Computing binding affinities of supramolecular host-guest systems
Hari S. Muddana, Michael K. Gilson.
10:30 389 Virtual docking and affinity prediction: Insights from benchmarking and validation studies
Enrico O. Purisima, Traian Sulea, Hervé Hogues.

COMP, Emilio Esposito, Scott Wildman Thursday, April 11, 2013 8:30 am - 11:15 am

Potential Function Uncertainty and Validation - AM Session Uncertainty Estimation
Morial Convention Center
Room: 356
Cosponsored by BIOL, CINF, MEDI, PHYS
John Faver, Kenneth Merz, Organizers
John Faver, Kenneth Merz, Presiding
8:30 450 Fragment-based methods for error estimation in biomolecular modeling
John C. Faver, Kenneth M. Merz.
9:00 451 Placing rigorous bounds on uncertainty in quantum chemical energy and structural optimisation calculations
Alistair P Rendell, Pete Janes.
9:30 452 Equilibrium simulations of protein folding as a force field test
Stefano Piana, Kresten Lindorff-Larsen, David E Shaw.
10:00   Intermission
10:15 453 Sensitivity and uncertainty analysis for dispersion-corrected density functional theory
Felix Hanke
10:45 454 Bayesian calibration of potential energy surfaces
Christopher S Simmons

COMP, Emilio Esposito, Scott Wildman Monday, April 8, 2013 1:30 pm - 4:45 pm

Protein-Ligand Interactions: Insights, New Tools and Applications in Drug Design - PM Session
Morial Convention Center
Room: 355
Cosponsored by BIOL, CINF, MEDI, PHYS
Rama Kondru, Sung-Sau So, Vickie Tsui, Organizers
Rama Kondru, Sung-Sau So, Vickie Tsui, Presiding
1:30 104 Alchemical calculations of binding free energies from MD simulations
David L Mobley, Gabriel J Rocklin.
2:00 105 Novel approaches to study protein-ligand interactions
Kenneth M Merz
2:30 106 Efficient optimization of enzyme inhibitors via free energy calculations
William L. Jorgensen
3:00   Intermission
3:15 107 Recognition of Gleevec by Src-family kinases
Benoit Roux, Yen-Lin Lin.
3:45 108 Computation of relative binding free energy for an inhibitor and its analogs binding with Erk kinase using thermodynamic integration MD simulation
Kuan-Wei Wu, Po-Chin Chen, Jun Wang, Ying-Chieh Sun.
4:15 pm 109 WITHDRAWN

COMP, Emilio Esposito, Scott Wildman Tuesday, April 9, 2013 8:30 am - 12:15 pm

Protein-Ligand Interactions: Insights, New Tools and Applications in Drug Design - AM Session
Morial Convention Center
Room: 355
Cosponsored by BIOL, CINF, MEDI, PHYS
Rama Kondru, Sung-Sau So, Vickie Tsui, Organizers
Rama Kondru, Sung-Sau So, Vickie Tsui, Presiding
8:30 144 MD and lead optimization: An evolving relationship
Christopher Bayly
9:00 145 Mechanism to trigger unfolding in alkylguanine alkyltransferase
Elizabeth Brunk, Birgit Mollwitz, Ursula Rothlisberger.
9:30 146 Withdrawn
10:00 147 Affixing the acylation gap: Elucidating DD-peptidase catalyzed beta-lactam reaction mechanisms
Jacqueline C. Hargis, Justin K. White, H. Lee Woodcock.
10:30   Intermission
10:45 148 Halogen bonding: From quantum chemistry to molecular design and chemical biology
Frank M. Boeckler, Rainer Wilcken, Markus O. Zimmermann, Andreas Lange, Andreas C. Joerger.
11:15 149 Heme-based nitric oxide release: Predicting reaction mechanisms via computational structure activity relationship studies
Sai Lakshmana Vankayala, Jacqueline C Hargis, Henry L Woodcock.
11:45 150 PDB ligand conformational energies calculated quantum-mechanically
Markus Sitzmann, Iwona E Weidlich, Igor V Filippov, Chenzhong Liao, Megan L Peach, Wolf-Dietrich Ihlenfeldt, Rajeshri G Karki, Yulia V Borodina, Raul E Cachau, Marc C Nicklaus.

COMP, Emilio Esposito, Scott Wildman Tuesday, April 9, 2013 1:30 pm - 5:45 pm

Protein-Ligand Interactions: Insights, New Tools and Applications in Drug Design - PM Session
Morial Convention Center
Room: 355
Cosponsored by BIOL, CINF, MEDI, PHYS
Vickie Tsui, Sung-Sau So, Rama Kondru, Organizers
Rama Kondru, Sung-Sau So, Vickie Tsui, Presiding
1:30 175 Accurate ligand docking and screening: Lessons from the Pocketome
Ruben Abagyan, Yu-chen Chen, Andrey Ilatovskiy, Irina Kufareva, Fiona McRobb, Manuel Rueda, Maxim Totrov.
2:00 176 Algorithms for discovering small molecules that stabilize specific protein conformations
Ryan G. Coleman, Marcus Fischer, Khanh Vuu, Brian K. Shoichet, James S. Fraser.
2:30 177 Novel methods to determine and exploit protein flexibility for ligand discovery
Marcus Fischer, Ryan G. Coleman, James S. Fraser, Brian K. Shoichet.
3:00 178 Flexible CDOCKER: Combining grid-based docking with pseudo-explicit structure based methods in CHARMM
Jessica K Gagnon, Charles L Brooks III.
3:30   Intermission
3:45 179 Can't wait for crystallography? Novel methods for GPCR loop prediction and docking
Dahlia A Goldfeld, Richard A Friesner.
4:15 180 Virtual screening against comparative protein structure models
Hao Fan, Andrej Sali, Brian K. Shoichet.
4:45 181 Wscore: An empirical scoring function for protein-ligand binding which incorporates the water structure of the active site
Richard A. Friesner
5:15 182 Unique electronic environment and contact direction sensitive scoring function for predicting affinities of protein-ligand complexes in Contour®
Suresh B Singh

COMP, Emilio Esposito, Scott Wildman Wednesday, April 10, 2013 8:30 am - 11:45 am

Protein-Ligand Interactions: Insights, New Tools and Applications in Drug Design - AM Session
Morial Convention Center
Room: 355
Cosponsored by BIOL, CINF, MEDI, PHYS
Rama Kondru, Sung-Sau So, Vickie Tsui, Organizers
Rama Kondru, Sung-Sau So, Vickie Tsui, Presiding
8:30 373 Consistent modeling of protein/nucleic acid small molecule interactions from free energies to ionization equilibrium
Charles L. Brooks III
9:00 374 Target-ligand interactions: Next generation modeling
Jose Duca, Robert Pearlstein, Daniel McKay.
9:30 375 Extending MixMD to allosteric systems
Phani Ghanakota, Heather A Carlson.
10:00   Intermission
10:15 376 Protein flexibility and ligand binding: Understanding the limitations of mapping protein surfaces
Heather A Carlson
10:45 377 Applications of 3D-RISM to structure-based drug design
Jean-François Truchon, Paul Labute.
11:15 378 Water displacement and conformational shifts in protein-ligand binding thermodynamics
Michael K. Gilson

COMP, Emilio Esposito, Scott Wildman Wednesday, April 10, 2013 1:30 pm - 5:15 pm

Protein-Ligand Interactions: Insights, New Tools and Applications in Drug Design - PM Session
Morial Convention Center
Room: 355
Cosponsored by BIOL, CINF, MEDI, PHYS
Rama Kondru, Sung-Sau So, Vickie Tsui, Organizers
Rama Kondru, Sung-Sau So, Vickie Tsui, Presiding
1:30 403 Investigation of the structural basis for the differential metabolism of glucocorticoids by CYP3A4 and CYP3A5 enzymes
Kiumars Shahrokh, Garold S Yost, Thomas E Cheatham III.
2:00 404 G-protein coupled receptors in virtual screening: Functional fidelity and selectivity
Dahlia R Weiss, SeungKirl Ahn, Maria F Sassano, Andrew C Kruse, Joel Karpiak, Bryan L Roth, Brian K Kobilka, Brian K Shoichet, Robert J Lefkowitz.
2:30 405 Toward the accurate and efficient identification of novel human soluble epoxide hydrolase inhibitors via in-silico methods
Camilo Velez-Vega, Crystal Nguyen, Michael K. Gilson, Sung-Hee Hwang, Kin Sing Stephen Lee, Bruce D. Hammock.
3:00 406 Designing and unraveling promiscuous inhibitors against drug-resistant target mutations
Yang Shen, Mala L Radhkarishnan, Bruce Tidor.
3:30   Intermission
3:45 407 How proteins bind macrocycles: Lessons for the design of macrocyclic compound libraries for drug discovery
Elizabeth A Villar, Dmitri Beglov, Sandor Vajda, Adrian Whitty.
4:15 408 Could it be magic? Unusual and interesting protein-ligand interactions
Martha S Head, Denise Pohlhaus.
4:45 409 Characterization of sulfotransferase specific metabolism using dynamic pharmacophores
Christin Rakers, Gerhard Wolber.

COMP, Emilio Esposito, Scott Wildman Thursday, April 11, 2013 8:30 am - 11:45 am

Protein-Ligand Interactions: Insights, New Tools and Applications in Drug Design - AM Session
Morial Convention Center
Room: 355
Cosponsored by BIOL, CINF, MEDI, PHYS
Rama Kondru, Sung-Sau So, Vickie Tsui, Organizers
Rama Kondru, Sung-Sau So, Vickie Tsui, Presiding
8:30 438 Applications of weighted ensemble molecular dynamics to free energy landscapes
Sreeja Parameswaran, David Mobley.
9:00 439 Annotating protein-ligand relationships with binding site surface similarity using Surflex-PSIM
Russell Spitzer, Ann E Cleves, Ajay N Jain.
9:30 440 Identifying binding hot-spots with molecular interaction networks
Bernd Kuhn, Neil R. Taylor.
10:00   Intermission
10:15 441 Necessity of clean data: Protein preparation in the GUI era
Carsten Detering
10:45 442 Expert protein-ligand interaction analysis delivered to chemist's desktop
Huifen Chen, Neil R. Taylor, Slaton Lipscomb, Jeff Blaney.
11:15 443 Structure-based drug design exploiting dynamic combinatorial chemistry to identify novel inhibitors for the aspartic protease endothiapepsin
Anna KH Hirsch