Binding-affinity predictions of HSP90 in the D3R Grand Challenge 2015 with docking, MM/GBSA, QM/MM, and free-energy simulations

Journal of Computer-Aided Molecular Design

Volumn 30, Issue 9, 2016, Pages 707-730

  Misini Ignjatović, Majda ^a   Caldararu, Octav ^a   Dong, Geng ^a   Muñoz Gutierrez, Camila ^b   Adasme Carreño, Francisco ^b   Ryde, Ulf ^a  

^a CHEMICAL CENTER   (Sweden)

^b UNIVERSIDAD DE TALCA   (Chile)

Author keywords

Bennett acceptance ratio; Big QM; Blind test competition; Continuum solvation; D3R grand challenge; Free energy perturbation; Induced fit docking; Ligand binding affinity; MM GBSA; QM MM

Indexed keywords

ACCEPTANCE TESTS; BINDING ENERGY; FREE ENERGY; MOLECULAR MECHANICS; MOLECULES; PROTEINS; QUANTUM THEORY; SOLVATION; SOLVENTS;

BENNETT ACCEPTANCE RATIO; BIG-QM; BLIND TEST; BLIND-TEST COMPETITION; CONTINUUM SOLVATIONS; D3R GRAND CHALLENGE; FREE ENERGY PERTURBATION; GRAND CHALLENGE; INDUCED FIT; INDUCED-FIT DOCKING; LIGAND BINDING AFFINITY; MM-GBSA; QUANTUM MECHANIC AND MOLECULAR MECHANIC;

LIGANDS;

HEAT SHOCK PROTEIN 90; HEAT SHOCK PROTEIN 90 INHIBITOR; LIGAND; SOLVENT; WATER; PROTEIN BINDING;

ARTICLE; BINDING AFFINITY; CALCULATION; COMPARATIVE STUDY; COMPUTER SIMULATION; CONTROLLED STUDY; CRYSTAL STRUCTURE; DISPERSION; ENERGY; ENTROPY; FREE ENERGY SIMULATION; GENERALISED BORN AND SOLVENT ACCESSIBLE SURFACE AREA SOLVATION; LIGAND BINDING; MOLECULAR DOCKING; MOLECULAR MECHANICS; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN INTERACTION; QUANTUM MECHANICS; RELATIVE BINDING AFFINITY; SOFTWARE; SOLVATION; STRUCTURE ANALYSIS; SURFACE AREA; BINDING SITE; CHEMISTRY; HUMAN; KINETICS; PROTEIN CONFORMATION; THERMODYNAMICS;

BINDING SITES; ENTROPY; HSP90 HEAT-SHOCK PROTEINS; HUMANS; KINETICS; LIGANDS; MOLECULAR DOCKING SIMULATION; PROTEIN BINDING; PROTEIN CONFORMATION; SOLVENTS; THERMODYNAMICS; WATER;

EID: 84983775745     PISSN: 0920654X     EISSN: 15734951     Source Type: Journal    
DOI: 10.1007/s10822-016-9942-z     Document Type: Article

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