Alchemical Grid Dock (AlGDock): Binding Free Energy Calculations between Flexible Ligands and Rigid Receptors.

ABSTRACT: Alchemical Grid Dock (AlGDock) is open-source software designed to compute the binding potential of mean force-the binding free energy between a flexible ligand and a rigid receptor-for a small organic ligand and a biological macromolecule. Multiple BPMFs can be used to rigorously compute binding affinities between flexible partners. AlGDock uses replica exchange between thermodynamic states at different temperatures and receptor-ligand interaction strengths. Receptor-ligand interaction energies are represented by interpolating precomputed grids. Thermodynamic states are adaptively initialized and adjusted on-the-fly to maintain adequate replica exchange rates. In demonstrative calculations, when the bound ligand is treated as fully solvated, AlGDock estimates BPMFs with a precision within

SUBMITTER: Minh DDL 

PROVIDER: S-EPMC7263302 | biostudies-literature | 2020 Mar

REPOSITORIES: biostudies-literature