TECHNICAL PROGRAM - American Chemical Society Publications

COMP TECHNICAL PROGRAM
Section F
Boston Convention & Exhibition Center
Room 154
Drug Discovery
High Throughput Screening: Robots Ruling
the Plates
S. Wildman, Y. Tseng, Organizers
S. Natesan, Presiding
8:30 107. Sticking to kinases: Scaffold selectivity
and implications for focused library
design. S. L. Posy, S. R. Johnson,
D. Loughney, M. Hermsmeier,
W. Vaccaro, G. Trainor, K. Ott
9:00 108. Novel classification of proteases
in the peptide substrate space reveals
cross-family substrate similarities with
applications to lead discovery.
S. K. Sukuru, F. Nigsch, J. Quancard,
M. Renatus, R. Chopra, N. Brooijmans,
D. Mikhailov, Z. Deng, A. Cornett,
J. L. Jenkins, U. Hommel, J. W. Davies,
M. Glick
9:30 109. Profile-QSAR and surrogate autoshim:
Utilizing chemogenomic relationships
for drug discovery applications.
P. Mukherjee, E. Martin
10:00 Intermission
10:15 110. Introduction of an interpretation
layer to link unsupervised and supervised
methods for classification of chemicals in
biological effects space. J. Rathman,
C. Yang
10:45 111. Creating reaction schemes to
generate an arbitrary number of linked
and conjugated polymers.
R. Olivares-Amaya, S. Atahan,
A. Aspuru-Guzik, C. A. Bedolla
Section G
Boston Convention & Exhibition Center
Room 153C
Waters: Feisty Little Molecules
E. X. Esposito, Organizer
K. Immadisetty, Presiding
8:30 112. Quantitative rate calculations from
simulations: The Ru 2� -Ru 3� electron
self-exchange reaction in water.
H. Oberhofer, J. Blumberger
9:00 113. “On water” reactivity and solvent
effects for Claisen rearrangements from
QM/MM simulations. O. Acevedo,
K. Armacost
9:30 114. Effect of hydrogen bonding on the
dynamical stability of water clusters.
J. R. Green, T. S. Hofer, D. J. Wales
10:00 Intermission
10:15 115. DFT geometry optimization and
vibrational frequencies of the quaternary
ammonium cation-water [N (CH 3) 4 � OH - /
(H 2O) n] clusters. D. Kumari,
E. S. Smotkin, N. Dimakis
10:45 116. Computational study of vibrational
spectra of some water containing
complexes of atmospheric interest.
E. Sälli, T. Salmi, L. Halonen
11:15 117. Using a vibrational averaging
technique to understand the role of water
dimers in atmospheric absorption.
R. E. Kelly, M. J. Barber, J. Tennyson,
G. C. Groenenboom, A. van der Avoird
Section C
Boston Convention & Exhibition Center
Room 157A
Challenges in Industrial Computational
Methods
42–TECH
A. Nicholls, E. Sourial, Organizers
C. Lemmen, C. Groom, Presiding
‡ Cooperative Cosponsorship
9:00 118. Modeling for the masses: The philosphers’
stone of CAMD software.
A. C. Good
10:00 119. Lightning-fast 3D-shape and feature-based
virtual screening. C. Lemmen
Section E
Boston Convention & Exhibition Center
Room 157B
The Community Structure-Activity
Resource (CSAR) Scoring Challenge
Cosponsored by BIOL, CINF, and MEDI
H. Carlson, Organizer, Presiding
9:00 Introductory Remarks
9:05 120. Community structure-activity resource:
Collecting, curating, and generating
protein-ligand data to improve docking
and scoring. J. B. Dunbar,
H. A. Carlson
9:35 121. Results of CSAR’s 2010 Benchmark
Exercise. J. B. Dunbar, R. D. Smith,
H. A. Carlson
10:05 122. Scoring performance of eHiTS
on the CSAR dataset. Z. Zsoldos,
O. Ravitz
10:35 Intermission
10:50 123. Hydrophobic complementarity: A
dominant term in affinity and binding
mode prediction. L. A. Kuhn,
M. E. Tonero
11:20 124. Docking and scoring for 2010
CSAR benchmark using an improved iterative
knowledge-based scoring function
with MDock. S. Huang, X. Zou
Chemical Computations on General
Purpose Graphics Processing Units (GP-
GPUs)
Electronic Structure Calculations on GPUs
Sponsored by PHYS, Cosponsored by COMP
Semantic Web in Chemistry
OWL Chemical Ontologies Sponsored by
CINF, Cosponsored by COMP
The Journal of Chemical Information and
Modeling’s 50th Anniversary Symposium
Sponsored by CINF, Cosponsored by COMP
MONDAY AFTERNOON
Section A
Boston Convention & Exhibition Center
Room 156C
Frontiers of Condensed Phase Theory and
Simulation: A Tribute to Bruce J. Berne
Thermodynamics and Dynamics of
Complex Systems Cosponsored by PHYS
G. Voth, J. Straub, M. Tuckerman,
Organizers
R. Silbey, Presiding
1:30 125. Quantum glass. D. Reichman
2:00 126. Energy transfer, coherence, and
decoherence in molecular aggregates.
R. J. Silbey
2:30 127. Local solvent environment dependent
electron transfer reactions in roomtemperature
ionic-liquids. C. J. Margulis
3:00 Intermission
3:15 128. Crystallization of hard aspherical
particles. A. Cacciuto
3:45 129. Fluctuations and the second law
of thermodynamics: What do we know
that Maxwell, Boltzmann and Gibbs did
not know? C. Jarzynski
4:15 130. Microscopic kinetic model exhibiting
chiral symmetry breaking.
F. H. Stillinger
Section B
Boston Convention & Exhibition Center
Room 156B
An Emerging Challenge in Multiscale
Modeling and Simulation: Mechanistic
Understandings
New Developments in Coarse-grain Theory
H. Guo, J. Chu, Organizers
M. Hagan, Presiding
1:30 131. Getting the right answer for the
right reason: Accurate and transferable
coarse-grained models from structural information.
W. G. Noid, W. Mullinax
2:00 132. Improved lattice models of the hydrophobic
effect. P. Varilly, A. J. Patel,
D. Chandler
2:30 133. Dissecting force interactions between
cellulose and ionic liquids by using
the iterative-YGB method. H. Cho,J.Chu
3:00 Intermission
3:15 134. Fluctuations, slow dynamics, and
ordering across length and time scales in
nanoparticle self-assembly.
P. L. Geissler, M. Gruenwald,
A. Widmer-Cooper
3:45 135. Generalized mean field theory of
coarse-graining. V. Krishna, L. Larini
4:15 136. Statistics in multiresolution modeling:
An application of Bayesian interference
in multiscale coarse-graining. P. Liu
Section C
Boston Convention & Exhibition Center
Room 157A
Challenges in Industrial Computational
Methods
A. Nicholls, E. Sourial, Organizers
C. Lemmen, C. Groom, Presiding
1:30 137. Risk assessment of chemicals and
prediction of metabolism. J. Gasteiger,
T. Kleinoeder, J. Marucszyk,
C. H. Schwab, A. Tarkhov, L. Terfloth
2:30 138. Considering protein structural
variations in molecular docking: Ensemble
docking with GOLD. J. Cole,
C. Groom
Section D
Boston Convention & Exhibition Center
Room 157C
The Journal of Chemical Information and
Modeling’s 50th Anniversary Symposium
Cosponsored by CINF
W. Jorgensen, Organizer, Presiding
1:30 Introductory Remarks
1:40 139. Configurational entropy and mechanical
stress in molecular recognition.
M. K. Gilson
2:10 140. Advancing anthrax toxin countermeasures
using topomeric searching and
virtual screening methodologies.
E. A. Amin, T. Chiu, D. J. Hook,
M. A. Walters, B. C. Finzel, J. Solberg,
S. Patil, T. W. Geders, S. Rangarajan,
R. Francis, X. Zhang
2:40 141. Model-free drug-like filters.
O.Ursu,C.G.Bologa,T. I. Oprea
3:10 Intermission
3:25 142. Chemocentric informatics: Enabling
bioactive compound discovery
through structural hypothesis fusion.
A. Tropsha
3:55 143. Computers and drug discovery:
From duds to $5B drugs. R. C. Glen
4:25 144. Weighting and fusion methods for
similarity-based virtual screening.
P. Willett, S. Arif, J. Holliday, N. Malim,
C. Mueller
Section E
Boston Convention & Exhibition Center
Room 157B
The Community Structure-Activity
Resource (CSAR) Scoring Challenge
Cosponsored by BIOL, CINF, and MEDI
H. Carlson, Organizer
J. Dunbar, Presiding
1:30 145. Lead Finder in the CSAR scoring
challenge. V. Stroylov, G. Chilov,
O. Stroganov, F. Novikov, V. Kulkov
2:00 146. Benchmark of solvated interaction
energy (SIE) scoring function on the
CSAR-2010 dataset. T. Sulea,Q.Cui,
H. Hogues, C. R. Corbeil, E. O. Purisima
2:30 147. Protonation states and scoring receptor-ligand
poses: It’s always the details.
E. X. Esposito
3:00 Intermission
3:15 148. Role of active-site solvent in protein-ligand
binding affinity calculations.
Y. Che, V. Shanmugasundaram
3:45 149. Flexible docking using a stochastic
rotamer library of ligands. F. Ding,
S. Yin, N. V. Dokholyan
4:15 150. Cheminformatics meets molecular
mechanics: A combined application of
knowledge based pose scoring and
physical force field-based hit scoring
functions improves the accuracy of virtual
screening. J. Hsieh, S. Yin, X. S. Wang,
S. Liu, N. V. Dokholyan, A. Tropsha
Section F
Boston Convention & Exhibition Center
Room 154
Using Waters Explicitly in Drug Discovery
Characterization and Applications
Cosponsored by CINF and MEDI
W. Sherman, Organizer
V. Shanmugasundaram, Organizer,
Presiding
1:30 Introductory Remarks - Veer Shanmugasundaram
1:35 151. Application of free energy methods
to water molecules in protein binding
sites. J. W. Essex, C. Barillari,
M. Bodnarchuk, R. Viner
2:15 152. Which waters are important and
how do we identify them? S. Bowden,
J. C. Cole, O. Korb, T. Olsson,
J. Liebescheutz, C. Groom
2:45 153. Free energies and entropies of
water molecules at protein-ligand interfaces.
S. W. Rick,H.Yu
3:15 Coffee Break
3:30 154. Role of water molecules in docking
studies of Cytochromes P450.
C. Oostenbrink
4:00 155. Modeling explicit waters in docking
and scoring. N. Huang
4:30 156. Desolvation/resolvation: A revolving
door that controls the rates of association/dissociation
of protein-ligand complexes?
Analysis of PCSK9-EGF-A
binding kinetics using WaterMap.
R. A. Pearlstein, Q. Hu, J. Zhou,
D. Yowe, J. Levell, B. Dale, V. Kaushik,
D. Daniels, S. Hanrahan, W. Sherman,
R. Abel
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