Comparison between self-guided langevin dynamics and molecular dynamics simulations for structure refinement of protein loop conformations

Journal of Computational Chemistry

Volumn 32, Issue 14, 2011, Pages 3014-3022

  Olson, Mark A ^a   Chaudhury, Sidhartha ^b   Lee, Michael S ^a,c  

^a UNITED STATES ARMY MEDICAL RESEARCH INSTITUTE OF INFECTIOUS DISEASES   (United States)

^b U S ARMY MEDICAL RESEARCH AND MATERIEL COMMAND   (United States)

^c U S ARMY RESEARCH LABORATORY   (United States)

Author keywords

comparative protein models; conformational sampling; protein variable regions; replica exchange methods

Indexed keywords

COARSE-GRAINED LATTICE MODELS; COMPARATIVE ANALYSIS; CONFORMATIONAL SAMPLING; CONFORMATIONAL SPACE; DATA SETS; EMPIRICAL FORCE; ENERGY FUNCTIONS; FORCE FIELDS; GENERALIZED BORN; IMPLICIT SOLVENT MODEL; LANGEVIN DYNAMICS; LOOP CONFORMATION; MD SIMULATION; MOLECULAR DYNAMICS SIMULATIONS; NATIVE STRUCTURES; PARAMETERIZED; POTENTIAL ENERGY LANDSCAPES; PREDICTION ACCURACY; PROTEIN MODELS; REFERENCE STATE; REPLICA EXCHANGE SIMULATION; REPLICA-EXCHANGE METHODS; ROOT-MEAN SQUARE DEVIATION; ROSETTA; SCORING METHODS; STATISTICAL POTENTIAL; STRUCTURE REFINEMENTS;

COMPUTER SIMULATION; DYNAMICS; FORECASTING; MOLECULAR DYNAMICS; PROTEINS;

CONFORMATIONS;

PROTEIN;

ALGORITHM; ARTICLE; BIOLOGY; CHEMISTRY; COMPARATIVE STUDY; COMPUTER PROGRAM; MOLECULAR DYNAMICS; PROTEIN CONFORMATION; THERMODYNAMICS;

ALGORITHMS; COMPUTATIONAL BIOLOGY; MOLECULAR DYNAMICS SIMULATION; PROTEIN CONFORMATION; PROTEINS; SOFTWARE; THERMODYNAMICS;

EID: 80052027212     PISSN: 01928651     EISSN: 1096987X     Source Type: Journal    
DOI: 10.1002/jcc.21883     Document Type: Article

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