TECHNICAL PROGRAM - American Chemical Society Publications

COMP TECHNICAL PROGRAM
Section C
Boston Convention & Exhibition Center
Room 157A
Challenges in Industrial Computational
Methods
A. Nicholls, E. Sourial, Organizers
C. Lemmen, C. Groom, Presiding
9:00 346. Software for drug discovery: Are
we solving the most relevant problems?
W. Walters
Simulation of Hybrid Interfaces and Multi-
Component Polymeric Materials
Biointerfaces Sponsored by PMSE,
Cosponsored by COMP
The Emerging Concepts of Activity
Landscapes and Activity Cliffs and their
Role in Drug Research Sponsored by CINF,
Cosponsored by COMP and MEDI
WEDNESDAY AFTERNOON
Section A
Boston Convention & Exhibition Center
Room 156C
Frontiers of Condensed Phase Theory and
Simulation: A Tribute to Bruce J. Berne
Applications to Nanoscale and
Biomolecular Systems Cosponsored by
PHYS
J. Straub, M. Tuckerman, Organizers
G. Voth, Organizer, Presiding
1:30 347. Base-by-base ratcheting of single
stranded DNA through a solid-state
nanopore: The DNA transistor. H. Peng,
B. Luan, S. Harrer, S. Polonsky,
S. Rossnagel, G. Martyna, G. Stolovitzky
2:00 348. Exploring landscapes for protein
allostery, binding, and folding: Effective
potentials, replica exchange dynamics,
and kinetic network models. R. Levy,
M. Andrec, E. Gallicchio, W. Zheng
2:30 349. Aging: Rejuvenation and the ultimate
fate of supercooled liquids.
P. G. Wolynes
3:00 Intermission
3:15 350. Millisecond-long molecular dynamics
simulations of proteins on a special-purpose
machine. D. E. Shaw
3:45 351. Application of Markov State Models
to dramatically enhance sampling of
complex biomolecular simulations.
V. Pande
4:15 352. Multiscale theory and simulation
of biomolecular systems. G. A. Voth
Section B
Boston Convention & Exhibition Center
Room 156B
An Emerging Challenge in Multiscale
Modeling and Simulation: Mechanistic
Understandings
Protein Dynamics
J. Chu, Organizer
H. Guo, Organizer, Presiding
1:30 353. Multi-scale simulation methods
for modeling two-step ligand-protein
binding processes. M. Kang, C. A. Chang
2:00 354. Multiscale simulations of F1-AT-
Pase. J. Pu, M. Karplus
2:30 355. Constructing a mechanistic model
for a processive cellulose-degrading enzyme
from molecular simulation.
G. T. Beckham, J. F. Matthews,
Y. J. Bomble, L. Bu, W. S. Adney,
M. E. Himmel, M. R. Nimlos,
M. F. Crowley
46–TECH
‡ Cooperative Cosponsorship
3:00 Intermission
3:15 356. Allostery of protein as determined
by dynamics fluctuations and correlations.
M. Liu
3:45 357. Investigating conformational
changes of biological macromolecules
using multi-resolution Markov State Models.
X. Huang
4:15 358. Discovering conformational substates
essential to protein function: A
multi-scale approach. A. Ramanathan,
C. J. Langmead, C. S. Chennubhotla,
P. K. Agarwal
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 Panel Discussion
Section D
Boston Convention & Exhibition Center
Room 157C
Scripting & Programming
Cross Pharma Collaboration in High
Performance Computing Financially
supported by Intel Corporation and Dell
Incorporated
E. Fluder, Z. Yang, Organizers
1:30 359. Introduction to cross pharma high
performance computing forum.
J. C. Morris,Z.Yang
2:00 360. Applications and use of cloud
computing in the pharmaceutical industry.
M. D. Miller, D. M. Powers,
G. Stiegler, J. M. M
2:30 361. Current trends of high performance
computing in Pharma. S. Litster,
J. Martin
3:00 362. Challenges of HPC and collaboration
opportunities in Pharma.
R. Stansfield, M. D. Miller
3:30 Intermission
3:45 Open Panel Discussion
Section E
Boston Convention & Exhibition Center
Room 157B
Docking & Scoring: What Have We Learned
and Where Are We Now?
Learnings from Docking and Scoring
Evaluations with a Pharmaceutically
Relevant Data Set
N. Nevins, G. Warren, G. McGaughey,
Organizers
1:30 Introductory Remarks
1:35 363. Importance of pharmaceutically
relevant benchmark data. C. Lemmen,
M. Gastreich, C. Detering, P. Oledzki
2:05 364. Insights from “real world” docking
with RosettaLigand. I. W. Davis
2:35 365. Recent experiences with molecular
docking in MOE. C. Williams,
P. Labute
3:05 Intermission
3:20 366. Advances in induced-fit docking:
What we have learned (and not learned)
from the GSK dataset. D. Shivakumar,
W. Sherman
3:50 367. Surflex-Dock and the GSK Dataset:
A retrospective. E. Metwally
4:20 368. How to build a better mousetrap:
Experiences with docking/scoring benchmarks
– including the GlaxoSmithKline
set – and what has been learned.
L. M. Westerhoff
4:50 Concluding Remarks
Section F
Boston Convention & Exhibition Center
Room 154
Emerging Technologies in Computational
Chemistry
Award Symposium Financially supported by
Schrödinger, Inc.
C. Breneman, Organizer, Presiding
1:30 Introductory Remarks
1:35 369. Pocket similarity: Are alpha carbons
enough? H. Feldman
2:05 370. Chemically meaningful net atomic
charges and atomic multipole moments
that reproduce the electrostatic potential
in periodic and nonperiodic materials.
T. A. Manz, D. S. Sholl
2:35 371. Ultrafast electrostatic similarity:
The sound of inevitability?
P. C. Hawkins, A. Nicholls
3:05 372. Bringing GPUs to mainstream molecular
dynamics packages, acceleration
of AMBER molecular dynamics simulations
using NVIDIA GPUs: Achieving high
performance without sacrificing accuracy.
R. C. Walker
3:35 Intermission
3:50 373. Quantum polarized fluctuating
charge (QPFC) model: A practical method
to include quantum mechanical ligand
polarizability in force-field-based molecular
simulation. S. Kimura, R. Rajamani,
D. R. Langley
4:20 374. Status of the ReaxFF reactive
forcefield: Development and applications.
A. C. van Duin, M. Russo, K. Joshi,
S. Kim, S. Agrawalla, A. Kamat,
A. Bharati, J. D. Kubicki
4:50 375. Parametrization of site-specific
force fields for computational enzymology.
G. Lamoureux
5:20 Judgement and Award
Simulation of Hybrid Interfaces and Multi-
Component Polymeric Materials
Multiscale Simulation of Polymeric
Materials Sponsored by PMSE, Cosponsored
by COMP
The Emerging Concepts of Activity
Landscapes and Activity Cliffs and their
Role in Drug Research Sponsored by CINF,
Cosponsored by COMP and MEDI
THURSDAY MORNING
Section C
Boston Convention & Exhibition Center
Room 157A
Targeting Gram-Negative Pathogens
Cosponsored by CINF and MEDI
J. Starr, Organizer
V. Shanmugasundaram, Organizer,
Presiding
8:00 Introductory Remarks - Veer Shanmugasundaram
8:05 376. Approaches to the treatment of
multidrug resistant gram negative infections.
M. C. Noe, S. J. Brickner, T. Gootz,
M. Huband, M. E. Flanagan, J. Mueller
8:45 377. Physicochemical property space
of antibiotics. H. E. Moser
9:15 378. Physicochemical properties correlated
with Gram-negative antibacterial
activity of compounds in the Pfizer corporate
library. J. T. Starr, R. Gupta,
V. Shanmugasundaram
9:45 379. Combining lessons from computational
design of gram positive antibacterials
with datamining to aid the design
of novel gram negative antibacterials.
C. J. Eyermann
10:15 Intermission
10:30 380. Targeting gram-negative pathogens:
Drug design to improve antibiotics
permeation? E. Hajjar, A. Kumar,
P. Ruggerone, M. Ceccarelli
11:00 381. Structure-based lead optimization
of novel bacterial type II topoisomerase
inhibitors. N. D. Pearson,Z.Yang,
B. D. Bax, M. N. Gwynn
11:30 382. Fragment-based development of
tetrazole inhibitors against class A betalactamase.
Y. Chen
Section A
Boston Convention & Exhibition Center
Room 156C
Materials, Polymers, and Nano-stuff
Materials Are Soooooo Much Cooler Than
the Twilight Saga
E. X. Esposito, Organizer
J. Kelley, Presiding
8:30 383. Elucidating the molecular mechanisms
underlying the nucleation and
growth of nanoparticles. K. D. Watson,
J. Persson, C. Desgranges,
J. Delhommelle
9:00 384. Molecular and mesoscale mechanisms
of Brittle Bone Disease (Osteogenesis
imperfecta): A computational materiomics
study. M. J. Buehler, M. Buehler
9:30 385. Mimicking coarse-grained simulations
without coarse-graining: Enhanced
sampling by damping short-range interactions.
F. Wang,D.Wei
10:00 Intermission
10:15 386. Mechanism of sliding clamp
opening by the clamp loader RFC: Insight
from atomistic simulations. I. Ivanov,
J. McCammon, J. A. Tainer
10:45 387. Spatial hetererogeneity in the
temperature of a rectangular nanorod
dragged across a surface. A. V. Popov,
R. Hernandez
11:15 388. Molecular dynamics simulations
of nanoparticles and surfactants at oil/
water interfaces: Chemisorption vs. physisorption.
S. O. Nielsen,C.T.Nguyen,
U. Ranatunga
Section B
Boston Convention & Exhibition Center
Room 156B
An Emerging Challenge in Multiscale
Modeling and Simulation: Mechanistic
Understandings
Biological Membranes and Nanosystems
J. Chu, Organizer
H. Guo, Organizer, Presiding
8:30 389. Aggregation dynamics of spherically-symmetric
reactive colloidal particles.
M. C. Hagy,S.J.Fitzwater,
T. H. Pierce, M. Schure, A. V. Popov,
R. Hernandez
9:00 390. Coarse-grained models for processes
that involve large-scale membrane
deformation. Q. Cui
9:30 391. Coarse-graining electrostatics in
multiscale molecular simulations.
D. Alemani, F. Collu, E. Spiga,
M. Cascella, M. Dal Peraro
10:00 Intermission
10:15 392. Understanding the cellulosome
and its assembly with coarse-grain modeling:
Toward improving the CBP process.
M. Crowley, Y. J. Bomble,
M. R. Nimlos, M. E. Himmel
10:45 393. Developing multiscale simulation
models to study aggregation in peptidebased
materials. C. Peter
11:15 394. Recent progress in multiscale
molecular dynamics simulation of soft
matter. B. Ensing,P.B.Moore,
S. O. Nielsen
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