Binding affinity estimation from restrained umbrella sampling simulations.

ABSTRACT: The protein-ligand binding affinity quantifies the binding strength between a protein and its ligand. Computer modeling and simulations can be used to estimate the binding affinity or binding free energy using data- or physics-driven methods or a combination thereof. Here we discuss a purely physics-based sampling approach based on biased molecular dynamics simulations. Our proposed method generalizes and simplifies previously suggested stratification strategies that use umbrella sampling or other enhanced sampling simulations with additional collective-variable-based restraints. The approach presented here uses a flexible scheme that can be easily tailored for any system of interest. We estimate the binding affinity of human fibroblast growth factor 1 to heparin hexasaccharide based on th

SUBMITTER: Govind Kumar V 

PROVIDER: S-EPMC10766565 | biostudies-literature | 2023 Jan

REPOSITORIES: biostudies-literature