Could MM-GBSA be accurate enough for calculation of absolute protein/ligand binding free energies?

Journal of Molecular Graphics and Modelling

Volumn 46, Issue , 2013, Pages 41-51

  Mulakala, Chandrika ^a   Viswanadhan, Vellarkad N ^a  

^a JUBILANT BIOSYS LTD   (India)

Author keywords

Absolute binding free energy; Free energy of binding; Implicit salvation; MM GBSA; Protein ligand binding

Indexed keywords

BINDING FREE ENERGY; DIELECTRIC MODELING; FREE ENERGY OF BINDING; IMPLICIT SALVATION; IMPLICIT SOLVATIONS; MM-GBSA; PROTEIN-LIGAND COMPLEXES; SYSTEMATIC ANALYSIS;

COMPLEXATION;

BINDING ENERGY;

LIGAND;

ACCURACY; ARTICLE; CALCULATION; DEGRADATION; ENERGY; GENERALIZED BORN SURFACE AREA; LIGAND BINDING; METHODOLOGY; MOLECULAR MECHANICS; PRIORITY JOURNAL; PROTEIN BINDING; SOLVATION;

ABSOLUTE BINDING FREE ENERGY; BACE; FREE ENERGY OF BINDING; GB; GBSA; GENERALIZED-BORN; GENERALIZED-BORN SURFACE AREA; IMPLICIT SOLVATION; MM; MM-GBSA; MOLECULAR MECHANICS; PDPK-1; PHOSPHOINOSITIDE-DEPENDENT KINASE-1; PROTEIN/LIGAND BINDING; SGB; SGB WITH HYDROPHOBIC TERM ADDED TO THE NON-POLAR SURFACE AREA TERM; SGB-NP; SGB-NP WITH A VARIABLE DIELECTRIC FORMULATION; SURFACE-AREA BASED GENERALIZED BORN; VSGB-1.0; VSGB-1.0 WITH AN IMPROVED ENERGY FUNCTION; VSGB-2.0; Β-SECRETASE;

3-PHOSPHOINOSITIDE-DEPENDENT PROTEIN KINASES; ALDEHYDE REDUCTASE; AMYLOID PRECURSOR PROTEIN SECRETASES; ANIMALS; ASPARTIC ACID ENDOPEPTIDASES; CATTLE; HUMANS; LIGANDS; LINEAR MODELS; MOLECULAR DOCKING SIMULATION; PROTEIN BINDING; PROTEINS; SOFTWARE; THERMODYNAMICS; TRYPSIN;

EID: 84885362304     PISSN: 10933263     EISSN: 18734243     Source Type: Journal    
DOI: 10.1016/j.jmgm.2013.09.005     Document Type: Article

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