Solvent interaction energy calculations on molecular dynamics trajectories: increasing the efficiency using systematic frame selection.

ABSTRACT: End-point methods such as linear interaction energy (LIE) analysis, molecular mechanics generalized Born solvent-accessible surface (MM/GBSA), and solvent interaction energy (SIE) analysis have become popular techniques to calculate the free energy associated with protein-ligand binding. Such methods typically use molecular dynamics (MD) simulations to generate an ensemble of protein structures that encompasses the bound and unbound states. The energy evaluation method (LIE, MM/GBSA, or SIE) is subsequently used to calculate the energy of each member of the ensemble, thus providing an estimate of the average free energy difference between the bound and unbound states. The workflow requiring both MD simulation and energy calculation for each frame and each trajectory proves to be computatio

SUBMITTER: Lill MA 

PROVIDER: S-EPMC3212856 | biostudies-literature | 2011 Oct

REPOSITORIES: biostudies-literature