An efficient algorithm calculating common solvent accessible volume.

ABSTRACT: The solvent accessible surface area and the solvent accessible volume are measurements commonly used in implicit solvent models to include the effect of forces exerted by solvents on the protein surfaces (or the atoms on protein surfaces). The two measurements have limitations in describing interactions between proteins (or proteins' atoms) mediated/bridged by solvents. This is because describing the interactions between proteins should be able to capture the chain of protein-solvent-protein interactions while the solvent accessible surface area or the solvent accessible volume can capture only protein-solvent interactions. If we represent the solvent as a continuous medium, we can consider an atom of a protein can effectively interact with the solvent within a certain distance from its su

SUBMITTER: Kim IJ 

PROVIDER: S-EPMC8936456 | biostudies-literature | 2022

REPOSITORIES: biostudies-literature