BPS Program Book 2014

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

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Biophysical Society 58 th Annual Meeting, San Francisco, California