Predicting Displaceable Water Sites Using Mixed-Solvent Molecular Dynamics.

ABSTRACT: Water molecules are an important factor in protein-ligand binding. Upon binding of a ligand with a protein's surface, waters can either be displaced by the ligand or may be conserved and possibly bridge interactions between the protein and ligand. Depending on the specific interactions made by the ligand, displacing waters can yield a gain in binding affinity. The extent to which binding affinity may increase is difficult to predict, as the favorable displacement of a water molecule is dependent on the site-specific interactions made by the water and the potential ligand. Several methods have been developed to predict the location of water sites on a protein's surface, but the majority of methods are not able to take into account both protein dynamics and the interactions made by specific

SUBMITTER: Graham SE 

PROVIDER: S-EPMC6190669 | biostudies-literature | 2018 Feb

REPOSITORIES: biostudies-literature