Accurate prediction of dynamic protein-ligand binding using P-score ranking.

ABSTRACT: Protein-ligand binding prediction typically relies on docking methodologies and associated scoring functions to propose the binding mode of a ligand in a biological target. Significant challenges are associated with this approach, including the flexibility of the protein-ligand system, solvent-mediated interactions, and associated entropy changes. In addition, scoring functions are only weakly accurate due to the short time required for calculating enthalpic and entropic binding interactions. The workflow described here attempts to address these limitations by combining supervised molecular dynamics with dynamical averaging quantum mechanics fragment molecular orbital. This combination significantly increased the ability to predict the experimental binding structure of protein-ligand compl

SUBMITTER: Ibrahim PEGF 

PROVIDER: S-EPMC11980828 | biostudies-literature | 2024 Jul

REPOSITORIES: biostudies-literature