Contributions of higher-order proximal distribution functions to solvent structure around proteins.

ABSTRACT: The proximal distribution function (pDF) quantifies the probability of finding a solvent molecule in the vicinity of solutes. The approach constitutes a hierarchically organized theory for constructing approximate solvation structures around solutes. Given the assumption of universality of atom cluster-specific solvation, reconstruction of the solvent distribution around arbitrary molecules provides a computationally convenient route to solvation thermodynamics. Previously, such solvent reconstructions usually considered the contribution of the nearest-neighbor distribution only. We extend the pDF reconstruction algorithm to terms including next-nearest-neighbor contribution. As a test, small molecules (alanine and butane) are examined. The analysis is then extended to include the protein

SUBMITTER: Yousefi R 

PROVIDER: S-EPMC8439718 | biostudies-literature | 2021 Sep

REPOSITORIES: biostudies-literature