Ab Initio prediction of protein-ligand binding structures by replica-exchange umbrella sampling simulations

Journal of Computational Chemistry

Volumn 32, Issue 13, 2011, Pages 2810-2821

  Kokubo, Hironori ^a   Tanaka, Toshimasa ^a   Okamoto, Yuko ^b  

^a TAKEDA PHARMACEUTICAL COMPANY LIMITED   (Japan)

^b NAGOYA UNIVERSITY   (Japan)

Author keywords

computer aided drug design; molecular dynamics; protein ligand binding; replica exchange umbrella sampling; structure prediction

Indexed keywords

AB INITIO PREDICTION; AVERAGE POTENTIAL; COMPUTER-AIDED DRUG DESIGN; ENERGY VALUE; EXPERIMENTAL DATA; FREE ENERGY LANDSCAPE; FREE-ENERGY STATE; GLOBAL MINIMA; LIGAND BINDING; MAJOR PRINCIPAL COMPONENT; POTENTIAL OF MEAN FORCE; PREDICTION METHODS; PROTEIN DATA BANK; PROTEIN-LIGAND BINDING; PROTEIN-LIGAND COMPLEXES; PUTATIVE BINDING SITES; REACTION COORDINATES; STRUCTURE PREDICTION; TEST CASE; UMBRELLA SAMPLING; WEIGHTED HISTOGRAM ANALYSIS METHOD;

COMPLEXATION; COMPUTER SIMULATION; FORECASTING; FREE ENERGY; LIGANDS; MOLECULAR DYNAMICS; PRINCIPAL COMPONENT ANALYSIS; PROTEINS; REACTION KINETICS;

BINDING ENERGY;

LIGAND; PROTEIN;

ARTICLE; CHEMICAL MODEL; CHEMICAL STRUCTURE; COMPUTER SIMULATION; DRUG DESIGN; METABOLISM; PROTEIN BINDING; PROTEIN DATABASE; THERMODYNAMICS;

COMPUTER SIMULATION; DATABASES, PROTEIN; DRUG DESIGN; LIGANDS; MODELS, CHEMICAL; MODELS, MOLECULAR; MOLECULAR STRUCTURE; PROTEIN BINDING; PROTEINS; THERMODYNAMICS;

EID: 79960303680     PISSN: 01928651     EISSN: 1096987X     Source Type: Journal    
DOI: 10.1002/jcc.21860     Document Type: Article

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