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Biophysical Society 59
th
Annual Meeting, Baltimore, Maryland
782-P
os
B
oard
B562
ENHANCED CONFORMATIONAL SAMPLING OF
CARBOHYDRATES USING BIASING POTENTIAL AND SOLUTE
TEMPERING REPLICA EXCHANGE: APPLICATION TO THE
N-GLYCAN ON THE HIV GP120 ENVELOPE PROTEIN.
Mingjun Yang
, Jing Huang, Alexander D. MacKerell Jr.
783-P
os
B
oard
B563
DMD4B-HYDRA: TOWARD A NOVEL DISCRETE MOLECULAR
DYNAMICS PROTEIN MODEL.
Derya Meral
, Brigita Urbanc
784-P
os
B
oard
B564
TETRAMOLECULAR PARALLEL G-QUADRUPLEX VALIDATION
SET FOR MOLECULAR DYNAMICS SIMULATION WITH
CHARMM 27 FORCE FIELD. Daniela Barragan,
Marcos V. Becerra
,
Miguel A. Mendez
785-P
os
B
oard
B565
SAMBE: THE NEWWEBSERVER FOR PREDICTING THE
EFFECT OF NSSNP ON THE PROTEIN-PROTEIN BINDING
FREE ENERGY.
Marharyta Petukh
, Jacon Morrison, Minghui Li, Anna
Panchenko, Emil Alexov
786-P
os
B
oard
B566
BIO.B-GEN: AN INITIAL SYSTEM GENERATOR FOR
BIOLOGICAL MOLECULAR SIMULATIONS.
Dmitri Rozmanov
,
Peter Tieleman
787-P
os
B
oard
B567
VALIDATION AND DEVELOPMENT OF THE FORCE
FIELD PARAMETERS FOR DRUG AND DRUG-LIKE
MOLECULES.
Katarzyna B. Koziara
, Martin Stroet, Alpeshkumar K.
Malde, Alan E. Mark
788-P
os
B
oard
B568
international
travel awardee
A NOVEL METHOD FOR FORCE-FIELD CALIBRATION BASED
ON MAXIMUM-LIKELIHOOD APPROACH AND THERMAL
UNFOLDING DATA. Bartłomiej Zaborowski, Dawid Jagieła, Adam K.
Sieradzan, Cezary R. Czaplewski, Anna Hałabis, Agnieszka Lewandowska,
Wioletta Żmudzińska, Stanisław Ołdziej,
Jozef A. Liwo
789-P
os
B
oard
B569
QUANTUM MECHANICAL MOLECULAR MECHANICAL
CALCULATIONS USING AMOEBA FORCE FIELDS.
Yihan Shao
,
Andrew Simmonett, Frank Pickard, Gerhard Koenig, Bernard Brooks
790-P
os
B
oard
B570
THE DO’S AND DO NOT’S OF A 100 MILLION ATOM
MOLECULAR DYNAMICS SIMULATION.
Abhishek Singharoy
,
Danielle Chandler, Jacob Durrant, Melih Sener, Rommie Amaro, Klaus
Schulten
791-P
os
B
oard
B571
MINIMALLY-BIASED METADYNAMICS METHOD TO SAMPLE
CONFORMATIONAL ENSEMBLES COMPATIBLE WITH
EXPERIMENTAL MEASUREMENTS.
Fabrizio Marinelli
, José D.
Faraldo-Gómez
792-P
os
B
oard
B572
EFFICIENT HIGH ACCURACY NON-BONDED INTERACTIONS
IN THE CHARMM SIMULATION PACKAGE.
Frank C. Pickard
,
Andrew Craig Simmonett, Bernard Rigoberto Brooks
793-P
os
B
oard
B573
TOWARDS A POLARIZABLE FORCE FIELD FOR RNA BASED ON
THE CLASSICAL DRUDE OSCILLATOR.
Justin A. Lemkul
, Alexey
Savelyev, Alexander D. MacKerell, Jr.
794-P
os
B
oard
B574
IMPLEMENTATION OF REPLICA-EXCHANGE UMBRELLA
SAMPLING TO THE DFTB+ SIMULATION PACKAGE.
Shingo Ito
,
Yuko Okamoto, Stephan Irle
795-P
os
B
oard
B575
CHARMM GUI MEMBRANE BUILDER UPDATES.
Xi Cheng
, Yifei
Qi, Jumin Lee, Sunhwan Jo, Wonpil Im
796-P
os
B
oard
B576
EXPERIMENTAL AND THEORETICAL APPROACHES TO THE
STUDY OF PROBE DIFFUSION IN MACROMOLECULAR
SOLUTIONS.
Preston Donovan
, Yasaman Chehreghanianzabi,
Muruhan Rathinam, Silviya Zustiak
797-P
os
B
oard
B577
A COUPLED TWO-DIMENSIONAL MAIN CHAIN TORSIONAL
POTENTIAL FOR PROTEIN DYNAMICS. Ya Gao, Yongxiu Li, John
Z.H. Zhang,
Ye Mei
798-P
os
B
oard
B578
MOLECULAR DYNAMICS SIMULATION OF PROTEIN CRYSTAL
WITH POLARIZED PROTEIN-SPECIFIC CHARGE. Yongxiu Li,
John Z.H. Zhang,
Ye Mei
799-P
os
B
oard
B579
EXTENSION OF THE CHARMM GENERAL FORCE FIELD TO
LINKED NITROGEN-CONTAINING HETREROAROMATIC
RINGS.
Lei Fang
, Ignacio Soteras Gutiérrez, Kenno Vanommeslaeghe,
Alexander D. MacKerell Jr.
800-P
os
B
oard
B580
PHASE DIAGRAM OF LIPID-CHOLESTEROL MIXTURE:
COMPARISON BETWEEN DIFFERENT FORCE FIELDS.
Fernando Favela-Rosales
, César Millán-Pacheco, Humberto Saint-
Martin, Mauricio D. Carbajal-Tinoco, Iván Ortega-Blake
801-P
os
B
oard
B581
NON-MARKOVIAN ANALYSES FOR EXTRACTING LONG-
TIME BEHAVIOR FROM MOLECULAR SIMULATION
TRAJECTORIES.
Ernesto Suarez
, Daniel M. Zuckerman
802-P
os
B
oard
B582
NEW DEVELOPMENTS IN THE COLLECTIVE VARIABLES
MODULE: MORE FLEXIBLE, MORE INTERACTIVE.
Giacomo Fiorin
, Jérôme Hénin
803-P
os
B
oard
B583
PARAMETRIZATION OF HALOGEN BONDS IN THE CHARMM
GENERAL FORCE FIELD.
Ignacio Soteras Gutierrez
804-P
os
B
oard
B584
LOOS: A TOOL FOR MAKING NEW TOOLS FOR ANALYZING
MOLECULAR SIMULATIONS.
Tod D. Romo
, Alan Grossfield
805-P
os
B
oard
B585
A SMOLUCHOWSKI EQUATION FOR FORCE-MODULATED
CHEMISTRY IN SINGLE MOLECULE PULLING
EXPERIMENTS.
Gianmarc Grazioli
, Ioan Andricioaei
806-P
os
B
oard
B586
CHARMM-GUI MARTINI MAKER FOR COARSE-GRAINED
SIMULATIONS.
Yifei Qi
, Xi Cheng, Wonpil Im
807-P
os
B
oard
B587
NECESSITY OF HIGH PHYSICAL RESOLUTION IN THE
DEVELOPMENT OF FLEXIBLE COARSE-GRAINED PROTEIN
MODELS.
ZhiGuang Jia
, Jianhan Chen