Identifying ligand binding sites and poses using GPU-accelerated Hamiltonian replica exchange molecular dynamics

Journal of Computer-Aided Molecular Design

Volumn 27, Issue 12, 2013, Pages 989-1007

  Wang, Kai ^a   Chodera, John D ^b   Yang, Yanzhi ^a   Shirts, Michael R ^a  

^a University of Virginia   (United States)

^b MEMORIAL SLOAN KETTERING CANCER CENTER   (United States)

Author keywords

Binding mode prediction; Binding site identification; Free energy calculation; GPU accelerated molecular dynamics; Hamiltonian replica exchange; Ligand binding

Indexed keywords

BINDING ENERGY; BINDING SITES; CRYSTAL STRUCTURE; FREE ENERGY; GRAPHICS PROCESSING UNIT; LIGANDS; MOLECULAR DYNAMICS; PHASE SPACE METHODS; PROTEINS;

ACCELERATED MOLECULAR DYNAMICS; BINDING MODE PREDICTION; BINDING MODES; BINDING SITE IDENTIFICATION; BINDING-SITES; FREE-ENERGY CALCULATIONS; GPU-ACCELERATED; GPU-ACCELERATED MOLECULAR DYNAMIC; HAMILTONIAN REPLICA EXCHANGE; LIGAND BINDING; REPLICA EXCHANGE; SITE IDENTIFICATION;

HAMILTONIANS;

LIGAND; LYSOZYME;

ARTICLE; BINDING SITE; CONTROLLED STUDY; CRYSTAL STRUCTURE; ENERGY; HAMILTONIAN REPLICA EXCHANGE MOLECULAR DYNAMICS SIMULATION; IMAGE PROCESSOR; LIGAND BINDING; MOLECULAR DYNAMICS; PRIORITY JOURNAL;

BACTERIOPHAGE T4; BINDING SITES; MODELS, MOLECULAR; MOLECULAR DYNAMICS SIMULATION; MURAMIDASE; PROTEIN BINDING; PROTEIN CONFORMATION; SOLVENTS; THERMODYNAMICS;

EID: 84891852541     PISSN: 0920654X     EISSN: 15734951     Source Type: Journal    
DOI: 10.1007/s10822-013-9689-8     Document Type: Article

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