Evaluation of protein-protein docking model structures using all-atom molecular dynamics simulations combined with the solution theory in the energy representation

Journal of Chemical Physics

Volumn 137, Issue 21, 2012, Pages

  Takemura, Kazuhiro ^a   Guo, Hao ^a,b   Sakuraba, Shun ^c,d   Matubayasi, Nobuyuki ^b,c   Kitao, Akio ^a,b  

^a UNIVERSITY OF TOKYO   (Japan)

^b JAPAN SCIENCE AND TECHNOLOGY AGENCY   (Japan)

^c KYOTO UNIVERSITY   (Japan)

^d INSTITUTE FOR MOLECULAR SCIENCE   (Japan)

Author keywords

[No Author keywords available]

Indexed keywords

BINDING FREE ENERGY; COMPLEX MODEL; COMPLEX STRUCTURE; ENERGY CALCULATION; ENERGY DISTRIBUTION FUNCTIONS; ENERGY REPRESENTATIONS; EXPLICIT WATER; MOLECULAR DYNAMICS SIMULATIONS; MONOMER STRUCTURES; MONOMERIC STRUCTURES; PROTEIN-PROTEIN COMPLEXES; PROTEIN-PROTEIN DOCKING; PURE WATER; RIGID-BODY DOCKING; SIDE-CHAINS; SOLUTION THEORY; SOLVATION FREE ENERGIES; STRUCTURE REFINEMENTS;

ATOMS; BINDING ENERGY; CONFORMATIONS; FREE ENERGY; MODEL STRUCTURES; MOLECULAR DYNAMICS; PROTEINS; SOLVATION;

CRYSTAL ATOMIC STRUCTURE;

PROTEIN; RIBONUCLEASE; RIBONUCLEASE SA3; SOLVENT; TRYPSIN; WATER;

ANIMAL; ARTICLE; CATTLE; CHEMISTRY; HYDROGEN BOND; METABOLISM; MOLECULAR DOCKING; MOLECULAR DYNAMICS; PROTEIN BINDING; PROTEIN CONFORMATION; SOLUTION AND SOLUBILITY; STATIC ELECTRICITY; THERMODYNAMICS;

ANIMALS; CATTLE; HYDROGEN BONDING; MOLECULAR DOCKING SIMULATION; MOLECULAR DYNAMICS SIMULATION; PROTEIN BINDING; PROTEIN CONFORMATION; PROTEINS; RIBONUCLEASES; SOLUTIONS; SOLVENTS; STATIC ELECTRICITY; THERMODYNAMICS; TRYPSIN; WATER;

EID: 84870950733     PISSN: 00219606     EISSN: None     Source Type: Journal    
DOI: 10.1063/1.4768901     Document Type: Article

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