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, |
9:00 | 2 |
New ways to mine disparate screening data in PubChem
Evan Bolton, bolton@ncbi.nlm.nih.gov, |
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. |
9:50 | 4 |
PubChem widgets
Lianyi Han, hanl@ncbi.nlm.nih.gov, |
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. |
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. |
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. |
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, |
8:50 | 9 |
Library spaces for scientific computing discovery and learning
Andrea Twiss-Brooks, atbrooks@uchicago.edu, |
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. |
9:40 | 11 |
From traditional library organization to functional structure: How does it benefit library users?
Erja Kajosalo, kajosalo@mit.edu, |
10:05 | Intermission | |
10:20 | 12 |
Holistic approaches to service: Connecting researchers to libraries through relationship building
Kiyomi D. Deards, Kdeards2@unl.edu, |
10:45 | 13 |
Ask for research alterations: Emerge with a custom fit
Jill E Wilson, jew248@cornell.edu, Leah R McEwen. |
11:10 | 14 |
Let's work together: ACS Publications author outreach initiatives and opportunities for libraries
Sara Rouhi, S_Rouhi@acs.org, |
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. |
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. |
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. |
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. |
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. |
4:25 | 20 |
Integrated cheminformatics software for visualizing and analyzing high-throughput screening data
Denis Fourches, fourches@email.unc.edu, Alexander Tropsha. |
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. |
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. |
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. |
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. |
3:50 | 25 |
CuLLR me collaboration: Models and tools for user-driven eLibraries
Dianne Dietrich, dd388@cornell.edu, Leah R McEwen. |
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. |
|
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. |
|
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, |
|
29 |
Discovery of TLR2 antagonists by virtual screening
Manuela S Murgueitio1, m.murgueitio@fu-berlin.de, Sandra Santos-Sierra2, Gerhard Wolber1. |
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. |
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. |
9:25 | 32 |
Analyzing screening and similarity searching outcome in light of multiple approaches to the same target
Tina Garyantes, garyante@optonline.net, |
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. |
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. |
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. |
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. |
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. |
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. |
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. |
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, |
10:30 | 41 |
Reproducible research applied to cheminformatics experiments
Paul J Kowalczyk, paul.kowalczyk@scynexis.com, |
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, |
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, |
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. |
2:25 | 45 |
Tracing pharmacophore determinants of natural- and nutritional-like components in epigenetics and metabolism
Alberto Del Rio, alberto.delrio@gmail.com, |
2:50 | 46 |
Reverse pharmacognosy: From molecules to active ingredients
Quoc Tuan Do, quoctuan.do@greenpharma.com, Sylvain Blondeau, Philippe Bernard. |
3:15 | 47 |
Flavor network: Exploring the principles of food pairing
Sebastian E Ahnert1, sea31@cam.ac.uk, Yong-Yeol Ahn2, Albert-Laszlo Barabasi3. |
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, |
4:15 | 49 |
Reaxys as an information resource for food chemistry
David Evans1, david.evans@reedelsevier.ch, Juergen Swienty-Busch2. |
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. |
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. |
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, |
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, |
2:05 | 54 |
From inception to collaboration to publication: A complete integrated research management platform for researchers
Judy Chen, j_chen@acs.org, |
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. |
3:20 | 56 |
We're not in Kansas anymore
Roger Schenck, rschenck@cas.org, |
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. |
4:20 | Intermission | |
4:30 | 58 |
Science comedian's guide to communicating science to general audiences
Brian Malow, brian.malow@naturalsciences.org, |
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, |
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, |
2:20 | 61 |
Cheminformatics career at the Royal Society of Chemistry, UK
Colin Batchelor, batchelorc@rsc.org, |
2:50 | 62 |
Patent law as a non-traditional career in chemistry
Sarah P Hasford, shasford@mcguirewoods.com, |
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, |
4:05 | 64 |
From the bench to the board
Rebecca Boudreaux, rebecca@oberonfuels.com, |
4:35 | 65 |
Political "science": Opportunities for chemists in science policy
Ticora V Jones, ticjones@usaid.gov, |
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, |
|
4 |
PubChem widgets
Lianyi Han, hanl@ncbi.nlm.nih.gov, |
|
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. |
|
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. |
|
19 |
How to highlight hits: Advances in visual data analytics tools for HTS data
Jesse A. Gordon, jesse.gordon@dotmatics.com, Jess Sager. |
|
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. |
|
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, |
|
29 |
Discovery of TLR2 antagonists by virtual screening
Manuela S Murgueitio1, m.murgueitio@fu-berlin.de, Sandra Santos-Sierra2, Gerhard Wolber1. |
|
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. |
|
32 |
Analyzing screening and similarity searching outcome in light of multiple approaches to the same target
Tina Garyantes, garyante@optonline.net, |
|
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. |
|
41 |
Reproducible research applied to cheminformatics experiments
Paul J Kowalczyk, paul.kowalczyk@scynexis.com, |
|
46 |
Reverse pharmacognosy: From molecules to active ingredients
Quoc Tuan Do, quoctuan.do@greenpharma.com, Sylvain Blondeau, Philippe Bernard. |
|
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, |
|
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. |
|
67 |
Navigation through chemogenomics data with SPID
Austin B Yongye1, José L Medina-Franco2, jose.medina.franco@gmail.com. |
|
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. |
|
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. |
|
72 |
About the impact of open access bioassay data on cheminformatic approaches
Barbara Zdrazil, barbara.zdrazil@univie.ac.at, Gerhard F. Ecker. |
|
80 |
PubChem BioAssay: A public database for chemical biology data
Yanli Wang, ywang@ncbi.nlm.nih.gov, |
|
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. |
|
89 |
Making hidden data discoverable: How to build effective drug discovery engines?
Sebastian Radestock, s.radestock@elsevier.com, Jürgen Swienty-Busch. |
|
92 |
Chemical science that underpins the Reaxys database
Juergen Swienty-Busch1, j.swienty-busch@elsevier.com, Pieder Caduff2, David Evans2. |
|
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. |
|
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. |
|
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. |
|
118 |
Mining frequent itemsets: Constructing topological pharmacophores using pharmacophore feature pairs
Paul J Kowalczyk, paul.kowalczyk@scynexis.com, |
|
119 |
Lexichem: Not another chemical nomenclature app
Edward O Cannon, ed.cannon@eyesopen.com, |
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. |
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. |
9:10 | 71 |
Pharmacological profiling of drugs by linking chemoinformatics and bioinformatics data
Olivier Taboureau, otab@cbs.dtu.dk, |
9:35 | 72 |
About the impact of open access bioassay data on cheminformatic approaches
Barbara Zdrazil, barbara.zdrazil@univie.ac.at, Gerhard F. Ecker. |
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. |
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. |
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, |
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. |
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, |
9:05 | 78 |
NCI/CADD chemical structure Web services
Markus Sitzmann, sitzmann@helix.nih.gov, Alexey V. Zakharov, Laura Guasch Pàmies, Marc C. Nicklaus. |
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. |
10:05 | Intermission | |
10:20 | 80 |
PubChem BioAssay: A public database for chemical biology data
Yanli Wang, ywang@ncbi.nlm.nih.gov, |
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. |
11:20 | 82 |
Architecture for an open science molecular compound database
Egon L Willighagen, egon.willighagen@maastrichtuniversity.nl, |
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, |
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. |
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. |
3:10 | 86 |
Roundtripping between small-molecule and biopolymer representations
Noel M O'Boyle1, noel@nextmovesoftware.com, Evan Bolton2, Roger A Sayle1. |
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. |
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. |
4:40 | 89 |
Making hidden data discoverable: How to build effective drug discovery engines?
Sebastian Radestock, s.radestock@elsevier.com, Jürgen Swienty-Busch. |
5:05 | 90 |
Applying the law of parsimony in molecular design
Alberto Del Rio, alberto.delrio@gmail.com, |
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. |
2:35 | 92 |
Chemical science that underpins the Reaxys database
Juergen Swienty-Busch1, j.swienty-busch@elsevier.com, Pieder Caduff2, David Evans2. |
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. |
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. |
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. |
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. |
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. |
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. |
9:35 | 99 |
Implementation of multi-criteria decision making (MCDM) tools in early drug discovery processes
Marie Ledecq, marie.ledecq@ucb.com, |
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. |
10:50 | 101 | Withdrawn |
11:20 | 102 |
Finding multi-parameter rules for successful optimization
Matthew Segall, matt.segall@optibrium.com, Iskander Yusof, Edmund Champness. |
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, |
9:05 | 104 |
Analysis of tautomerism in databases of commercially available compounds
Laura Guasch, lguasch@helix.nih.gov, Markus Sitzmann, Marc C Nicklaus. |
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. |
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. |
10:50 | 107 |
One size fits all or how to find the needle in the haystack?
Juergen Swienty-Busch, j.swienty-busch@elsevier.com, |
11:20 | 108 |
Pistoia Alliance AppStore: Apps for life sciences R&D
Alex M Clark, aclark@molmatinf.com, |
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. |
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. |
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. |
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, |
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. |
2:25 | 114 |
PubChem3D: A virtual screening platform
Evan Bolton, bolton@ncbi.nlm.nih.gov, |
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. |
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. |
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. |
4:20 | 118 |
Mining frequent itemsets: Constructing topological pharmacophores using pharmacophore feature pairs
Paul J Kowalczyk, paul.kowalczyk@scynexis.com, |
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, |
8:30 | 120 |
Teach our naming tool to be bilingual: Chinese name-to-structure conversion
David Deng, ddeng@chemaxon.com, Daniel Bonniot. |
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. |
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
COMP, Emilio Esposito, Scott Wildman Monday, April 8, 2013 1:30 pm - 5:15 pm
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 |
- Printer-friendly version
- 10917 reads