TECHNICAL PROGRAM - American Chemical Society Publications

COMP TECHNICAL PROGRAM
1:30 205. Peptide partitioning properties
from direct water-to-membrane insertion
studies. J. P. Ulmschneider
2:00 206. Understanding interactions of propylene
glycol and skin lipids using molecular
dynamics simulation. J. Ghosh,
B. Michniak-Kohn
2:30 207. Conformational prediction of the
HIV-1 gp41 membrane-spanning domain.
V. K. Gangupomu,C.F.Abrams
3:00 208. Computing dynamics, electrostatics
and spectroscopy at membrane-water
interfaces. J. D. Hirst, D. Robinson,
N. A. Besley, P. O’Shea
3:30 Intermission
3:45 209. Lipid10: A comprehensive phospholipid
force field for AMBER.
R. C. Walker, A. Skjevik, K. Teigen
4:15 210. Adaptive multiscale modeling of
bilayer systems. P. B. Moore, V. Perez,
S. O. Nielsen, B. Ensing
4:45 211. Effect of spherical fullerenes on
pulmonary lipid monolayers: Molecular
dynamics simulations. S. O. Nielsen,
C. Chiu, P. B. Moore, R. DeVane,
M. L. Klein, W. Shinoda
Section E
Boston Convention & Exhibition Center
Room 157B
Docking & Scoring: What Have We Learned
and Where Are We Now?
Computational Approaches for Fragment
Screening
N. Nevins, G. Warren, Organizers
G. McGaughey, Organizer, Presiding
1:30 212. Fragment docking in BACE: Retrospective
survey of loop sampling and
docking. J. H. Voigt, P. Orth, Y. Wang,
D. Wyss, S. Babu, J. Caldwell,
S. Chackalamannil, X. Che, J. Cumming,
M. Czarniecki, J. Duo, J. Durkin, H. Gu,
T. Guo, R. Hunter, U. Iserloh,
M. E. Kennedy, R. Kuvelkar, L. Thuy,
V. Madison, R. D. Mazzola,
B. A. McKittrick, T. Meng, J. Misiaszek,
T. Nechuta, J. Pan, E. Parker, G. Qian,
K. Saionz, M. Senior, E. M. Smith, Z. Sun,
D. Tadesse, L. Wang, J. Wong, Y. Wu,
Y. Xia, Y. Ye, J. Zhao, Z. Zhu,
A. Stamford, W. Greenlee, C. Strickland
2:00 213. Accurate pose prediction and improved
structure-based virtual screening
for fragments. W. Sherman
2:30 214. Fragment screening paradigm for
drug discovery. D. Joseph-McCarthy
3:00 Intermission
3:15 215. Fragment-based druggability
measures in drug targets. D. R. Hall,
C. Ngan, B. Zerbe, D. Kozakov, S. Vajda
3:45 216. FragVLib: Fragment-based virtual
screening library using geometric and
chemical patterns of interactions at interface
of ligand-receptor complex crystal
structures. R. S. Khashan, W. Zheng
Section F
Boston Convention & Exhibition Center
Room 154
Using Waters Explicitly in Drug Discovery
Hybrid Explicit/Implicit Methods
Cosponsored by CINF and MEDI
V. Shanmugasundaram, Organizer
W. Sherman, Organizer, Presiding
1:30 Introductory Remarks - Woody Sherman
1:35 217. Molecular dynamics studies of
water-protein interactions. G. Hummer,
J. C. Rasaiah, H. Yin, G. Feng
44–TECH
‡ Cooperative Cosponsorship
2:15 218. Addressing limitations with the
MM-GB/SA scoring procedure using the
WaterMap method and free-energy perturbation
calculations. C. R. Guimaraes
2:45 219. Prediction of potency of protease
inhibitors by GBSA simulations with polarizable
quantum mechanics-based ligand
charges and a hybrid water model.
D. Das, H. Mitsuya, Y. Koh, Y. Tojo,
A. Ghosh
3:15 Coffee Break
3:30 220. Continuum theory and the analysis
of active sites. A. Nicholls,M.Word
4:00 221. Prediction of consistent water networks
in uncomplexed protein binding
sites based on knowledge-based potentials.
M. Betz, G. Neudert, G. Klebe
4:30 222. Explicit-water modeling of a
model protein-ligand binding site predicts
the non-classical hydrophobic effect.
D. T. Moustakas,P.W.Snyder,
W. Sherman, G. M. Whitesides
5:00 223. New coarse-grained model for
water: The importance of electrostatic interactions.
Z. Wu, Q. Cui, A. Yethiraj
TUESDAY EVENING
Section A
Boston Convention & Exhibition Center
Room 156B
Chemical Computing Group Excellence
Award Financially supported by Chemical
Computing Group, Inc
C. Simmerling, Organizer
6:00 224. Virtual screening targeting the
PhoP response regulator to inhibit bacterial
virulence. Y. T. Tang, E. A. Groisman,
J. J. Havranek, G. R. Marshall
6:20 225. Computational investigation of the
transport mechanism for monoamine
transporters. B. A. Merchant,
J. D. Madura
6:40 226. Quantum chemistry calculations
for arbitrarily complex electrostatic environments:
Benzene anion stabilization.
R. Olivares-Amaya, M. Stopa,
A. Aspuru-Guzik
7:00 227. Biomolecular dynamics simulations
based on the finite-difference Poisson-Boltzmann
method. Q. Cai,X.Ye,
J. Wang, M. Hsieh, R. Luo
7:20 228. Filtering and ranking enzyme designs
using EDGE. S. A. Johnson,
K. N. Houk
Section B
Boston Convention & Exhibition Center
Room 156B
Hewlett-Packard Outstanding Junior
Faculty Award Financially supported by
Hewlett-Packard Development Company, L.P.
C. Simmerling, Organizer
6:00 229. Quantum information and quantum
computation for chemistry.
A. Aspuru-Guzik
6:20 230. Excited-state quantum chemistry
for macromolecules and condensed
phases. J. M. Herbert
6:40 231. Mimicking coarse-grained simulations
without coarse-graining: Enhanced
sampling by damping short-range interactions.
F. Wang
7:00 232. Information flow in biomolecules.
A. van der Vaart
Section C
Boston Convention & Exhibition Center
Room 052A/B
Poster Session
E. X. Esposito, Organizer
6:00–8:00
233. Predicting the structure and the binding
site of rimonabant for the cannabinoid
CB1 receptor. C. E. Scott, R. Abrol,
W. A. Goddard
234. Theoretical studies of hydrogen spillover
mechanism for developing next generation
automobile catalyst: A quantum
chemical molecular dynamics study.
F. Ahmed, R. Muira, A. Suzuki, H. Tsuboi,
N. Hatakeyama, A. Endou, H. Takaba,
M. Kubo, A. Miyamoto
235. Crystallization of polydisperse systems
of aspherical particles. W. L. Miller,
A. Cacciuto
236. Dependent of structural and thermodynamic
characteristics of supercritical carbon
dioxide fluid from atomic charges in
molecule in region of critical point calculated
by RISM theory. S. V. Keshtova,
F. Keshtova
237. Application of structure and ligand
based methods for the investigation of
the flexibility of loop regions within a cyclin-dependent
kinase (CDK) and the prediction
of a possible binding mode of
highly selective inhibitors. C. Jäger,
M. Buchholz, W. Brandt, L. Zeitlmann,
A. Niestroj, H. Demuth, U. Heiser
238. Molecular simulation of the nucleation
and growth of C60 nanoparticles from the
supersaturated vapor and from the undercooled
liquid. K. Ngale,
C. Desgranges, J. Delhommelle
239. Phase equilibria of polyaromatic hydrocarbons
by hybrid Monte Carlo Wang-
Landau simulations. A. Magness,
C. Desgranges, J. Delhommelle, J. Hicks
240. Molecular simulation of the formation of
Fe-Pt nanomaterials for ultrahigh-density
magnetic data storage. J. Persson,
C. Desgranges, J. Delhommelle
241. Enhanced sampling in folding simulations
of Ala5 peptide by DSRI method.
D. Wei,F.Wang
242. Monte Carlo statistical analysis of the
uncertainty of enrichment metrics for ensemble
docking. I. Tubert-Brohman
243. Docking studies of propafenone derivatives
into a homology model of the hERG
channel in the open state. A. Schiesaro,
A. Windisch, E. Eugen Timin, S. Hering,
G. F. Ecker
244. QSAR, ligand efficiency (LE) and lipophilic
efficiency (LipE) studies of a series
of benzophenone-type inhibitors of
the multidrug transporter P-glycoprotein.
I. Jabeen, Z. Parveen, U. Rinner,
P. Chiba, G. F. Ecker
245. Molecular insight into FabH-inhibitor interactions
using molecular dynamics simulations
and free energy calculations to
identify novel scaffolds for inhibition by
pharmacophore-based virtual screening.
A. Mittal, M. E. Johnson
246. Molecular origin of the interaction between
PB1 and PB2 subunit in RNA polymerase
of influenza virus. J. Park,W.Jo
247. Development of minimal pharmacophore
hypotheses by molecular dynamics
simulation and spatial restriction for
screening N5-CAIR mutase fragment-like
inhibitors. T. Zhu, D. Mulhearn,
M. E. Johnson
248. Computational modeling study of anthranilate
synthase from Streptomyces
venezuelae for the developing new antimicrobial
agents. J. Z. Hu, M. Ashenafi,
W. M. Byrnes, W. W. Southerland
249. Machine learning application for the
high-performance prediction of functional
sites in proteins of unknown function.
S. Somarowthu,Y.Wang,
A. Michaelson, H. Yang, M. Ondrechen
250. Identification of functional subclasses in
the ribulose-phosphate binding barrel superfamily
using computational tools.
J. S. Lee, S. Somarowthu, M. Ondrechen
251. Comparison of the performance of different
scoring functions in docking of antidepressants
to serotonin transporter.
S. G. Manepalli, J. D. Madura, C. Surratt
252. Novel scaffold replacement methodology
applied to the discovery of P38 MAP
kinase inhibitors. J. Leonard,
N. Thorsteinson
253. Insights into the cross-reaction between
trypanosoma cruzi antibodies and
human beta-1 adrenergic receptor.
C. F. de Oliveira, A. J. McCammon
254. Molecular orbital study of keto-enol tautomerism
of salvinorin A models. I. Vinar,
W. J. Skawinski, C. A. Venanzi
255. Ligand-steered modeling of the cannabinoid
receptor 2: Successful applications
to rationalize SAR data of selective
CB2 inverse agonist and agonist compounds.
S. S. Phatak, P. Diaz, J. Xu,
F. Astruc-Diaz, M. Naguib,
C. N. Cavasotto
256. Development of property-encoded
shape distribution descriptors for the robust
prediction of polymer glass transition
temperatures. M. P. Krein,S.Das,
M. J. Embrechts, B. Natarajan,
L. Schadler, C. M. Breneman
257. Molecular dynamics studies of amphiphathic
peptides embedded within a
lipid bilayer. T. T. Nguyen, Z. Liu,
P. B. Moore
258. Structural basis of pregnane X receptor
binding promiscuity. C. Ngan, D. Beglov,
A. N. Rudnitskaya, D. Kozakov,
D. J. Waxman, S. Vajda
259. Coarse-grained modeling of antibody
self-association. A. Chaudhri,
T. Kamerzell, G. A. Voth
260. An N log N generalize Born approximation.
R. Anandakrishnan, A. V. Onufriev
261. Development of internal potentials for a
protein coarse-grain forcefield.
K. Nguyen, J. Galan, Z. Liu, R. DeVane,
P. Moore
262. Interaction of 12c4 with alkali metal cation
in aqueous solution: Theoretical investigation
using polarized continuum
model. T. Arora, H. Ali, W. A. Burns,
H. Koizumi
263. LowModeMD: Conformational search
of small molecules, macrocycles, and
protein loops. E. Sourial,P.Labute
264. Parameterization of small drug-Like ligands
using CHARMM General Force
Field. K. C. Immadisetty, J. Gibbons,
J. Brancho, J. D. Madura
265. Glycogen phosphorylase inhibitor identification
targeting the inhibitor binding
site using virtual screening and experimental
validation. S. Zhong, K. Alexacou,
M. A. Charavgi, C. Tiraidis,
S. E. Zographos, D. D. Leonidas,
E. D. Chrysina, N. G. Oikonomakos,
A. D. MacKerell, Jr.
266. Structure refinement by J-coupling constants
restraining using local elevation.
D. Steiner, W. F. van Gunsteren
267. First-principles design of conductance
switching in functionalized carbon nanotubes.
E. Y. Li, N. Poilvert, N. Marzari
268. Binding free energy of cocaine and citalopram
to the serotonin transporter using
molecular dynamics. J. J. Brancho,
K. Immadisetty, J. Gibbons, J. D. Madura
269. Prediction of Lapatinib selectivity with
kinases in the ErbB family. Y. Huang
270. Correcting for errors in one-body and
two-body interactions of small molecules
in DFT with empirical potential forms parameterized
through force matching.
Y. Song,F.Wang
271. Identification of novel non-hydroxamate
anthrax toxin lethal factor inhibitor scaffolds
using in silico and in vitro highthroughput
screening methodologies.
T. Chiu, J. Solberg, S. Patil,
T. W. Geders, X. Zhang, S. Rangarajan,
R. Francis, B. C. Finzel, M. A. Walters,
D. J. Hook, E. A. Amin
272. HS-PHARM-GEN: An automated tool
for generating receptor-based pharmacophores
from ligand-free protein structures.
G. Chuang, C. Barillari, D. Rognan
273. Molecular interaction footprints: A
docking rescoring method. T. E. Balius,
S. Mukherjee, R. C. Rizzo
Photographing or recording
meeting sessions and/or
activities other than your own
are prohibited at all official
ACS events without written
consent from ACS.