111
Biophysical Society 58
th
Annual Meeting, San Francisco, California
M
O
N
D
A
Y
2052-P
os
B
oard
#B782
MANAGEMENT OF MOLECULAR SIMULATION DATA-
BASE. Anand Kumar,
Yicheng Tu
, Sagar Pandit
2053-P
os
B
oard
#B783
ST-ANALYZER: A WEB-BASED USER INTERFACE FOR
SIMULATION TRAJECTORY ANALYSIS.
Jong Cheol Jeong
,
Sunhwan Jo, Emilia L Wu, Yifei Qi, Viviana Monje, Min Sun Yeom,
Lev Gorenstein, Feng Chen, Jeffery B. Klauda, Wonpil Im
Computational Methods I
(Boards #B784–#B813)
2054-P
os
B
oard
#B784
MODIFIED FAST MULTIPOLE METHOD FOR COARSE-GRAINED
MOLECULAR SIMULATIONS.
Mohammad Poursina
2055-P
os
B
oard
#B785
BIOMOLECULAR STRUCTURE REFINEMENT & PREDICTION
USING DEAD-END ELIMINATION WITH A POLARIZABLE
FORCE FIELD. Stephen D. LuCore, Shibo Gao, Ava M. Lynn,
WilliamT. A. Tollefson, KyleT. Powers, Timothy D. Fenn,
Michael J. Schnieders
2056-P
os
B
oard
#B786
IMPROVING THE COMPUTATIONAL EFFICIENCY OF THE
INDUCED-DIPOLE MODEL IN AMOEBA VIA THE 3-BODY
APPROXIMATION.
Omar Demerdash
, Liam D. O’Suilleabhain,
Teresa L. Head-Gordon
2057-P
os
B
oard
#B787
MULTIPOLES AS FORCE FIELD PARAMETERS - ACCURACY AND
REDUNDANCY.
Sofie Jakobsen
2058-P
os
B
oard
#B788
ASSESSMENT OF NONPOLAR TERMS IN IMPLICIT SOLVENT
MODELS TO ESTIMATE SMALL MOLECULE HYDRATION FREE
ENERGIES.
Martin Brieg
, Julia Setzler, Wolfgang Wenzel
2059-P
os
B
oard
#B789
SIZE-MODIFIED POISSON-BOLTZMANN ELECTROSTATICS
FOR REALISTIC BIOMOLECULAR SYSTEMS.
Nuo Wang
,
Peter Kekenes-Huskey, Shenggao Zhou, Bo Li, J. Andrew McCammon
2060-P
os
B
oard
#B790
FREE-ENERGY CALCULATIONS FOR SEMI-FLEXIBLE
MACROMOLECULES: APPLICATIONS TO DNA KNOTTING
AND LOOPING.
Stefan M. Giovan
, Robert G. Scharein,
Andreas Hanke, Stephen D. Levene
2061-P
os
B
oard
#B791
FREE ENERGY CALCULATION OF PROTEIN CONFORMATIONAL
CHANGES USING PARALLEL CASCADE SELECTIONMOLECULAR
DYNAMICS SIMULATION AND MARKOV STATE MODEL.
Yasutaka Nishihara
, Ryuhei Harada, Akio Kitao
2062-P
os
B
oard
#B792
international
travel
awardee
A COMPUTATIONAL METHOD INCLUDING PROTEIN
FLEXIBILITY TO ESTIMATE AFFINITIES WITH SMALL
LIGANDS.
Ariane Nunes-Alves
, Guilherme M. Arantes
2063-P
os
B
oard
#B793
DEVELOPMENT OF EFFICIENT ENERGY FUNCTION FOR
PROTEIN-SMALL MOLECULE INTERACTIONS IN
MEDUSADOCK.
Praveen Nedumpully Govindan
, Feng Ding
2064-P
os
B
oard
#B794
CONFORMATIONAL CONTRIBUTION TO THERMODYNAMICS
OF BINDING IN PROTEIN COMPLEXES THROUGH
MICROSCOPIC SIMULATIONS.
Jaydeb Chakrabarti
, Amit Das,
Mahua Ghosh
2065-P
os
B
oard
#B795
STRUCTURE-BASED PREDICTORS OF RESISTANCE TO THE
HIV-1 INTEGRASE INHIBITOR ELVITEGRAVIR.
Majid Masso
,
Grace Chuang, Shinar Jain, Kate Hao, Iosif I. Vaisman
2066-P
os
B
oard
#B796
ELUCIDATING EPHRIN-INDUCED INTERSECTING SIGNALING
PATHWAYS INTHE NIPAHVIRUS G PROTEIN USINGMACHINE
LEARNING.
Mohsen Botlani
, Ralph Leighty, Sameer Varma
2067-P
os
B
oard
#B797
DESIGN OF DRUGLIKE SMALL MOLECULES WITH
LYN-SPECIFIC BINDING.
D. S. Dalafave
2068-P
os
B
oard
#B798
EFFECT OF CRYSTAL METH AND ECSTASY ENANTIOMERS
ON FUNCTION OF DOPAMINE TRANSPORTERS.
Igor Zdravkovic
, Sergei Y. Noskov
2069-P
os
B
oard
#B799
PREDICTING DRUGGABLE SITES IN PROTEIN-PROTEIN
INTERFACES USING
FINDBINDSITE
.
Hubert Li
, Vinod Kasam,
Nagarajan Vaidehi
2070-P
os
B
oard
#B800
UNDERSTANDING THE INTERACTIONS OF THREE
INTEGRINS WITH A LIBRARY OF PEPTIDES.
Matt McKenzie
,
Aravind R. Rammohan
2071-P
os
B
oard
#B801
RE-DOCKING SCHEME TO EXPLORE DOCKING SEARCH
SPACE BY USING INTERACTION PROFILES.
Nobuyuki Uchikoga
,
Yuri Matsuzaki, Masahito Ohue, Takatsugu Hirokawa, Yutaka Akiyama
2072-P
os
B
oard
#B802
MODEL OF THE NOGO: NOGO RECEPTOR COMPLEX.
Ali Alhoshani
, Rosemarie Vithayathil, Gregory A. Weiss, Melanie J Cocco
2073-P
os
B
oard
#B803
BIOMOLECULAR RECOGNITION BASED ON 3D MOLECULAR
THEORY OF SOLVATION.
Nikolay Blinov
, Wenjuan Huang,
Dragan Nikolic, David S. Wishart, Andriy Kovalenko
2074-P
os
B
oard
#B804
FLUCTUATION FLOODING METHOD (FFM) FOR ENHANCING
CONFORMATIONAL SAMPLING OF PROTEINS.
Ryuhei Harada
2075-P
os
B
oard
#B805
ACCELERATING THE MOLECULAR DYNAMICS SAMPLING
OF MUTANTS: A HIERARCHICAL BAYESIAN MARKOV STATE
MODEL STRATEGY.
Robert T. McGibbon
, Vijay S. Pande
2076-P
os
B
oard
#B806
PREDICTING HLA-SPECIFIC DRUG HYPERSENSITIVITY WITH
MOLECULAR DOCKING AND MOLECULAR DYNAMICS
SIMULATIONS.
Xin-Qiu Yao
, Barry J. Grant
2077-P
os
B
oard
#B807
GENERALIZED SCALABLE MULTIPLE COPY ALGORITHMS
FOR BIOLOGICAL MOLECULAR DYNAMICS SIMULATIONS IN
NAMD.
Wei Jiang
, James Phillips, Lei Huang, Mikolai Fajer, Yilin Meng,
James C. Gumbart, Yun Luo, Klaus Schulten, Benoit Roux
