Solvation Free Energy as a Measure of Hydrophobicity: Application to Serine Protease Binding Interfaces.

ABSTRACT: Solvation and hydrophobicity play a key role in a variety of biological mechanisms. In substrate binding, but also in structure-based drug design, the thermodynamic properties of water molecules surrounding a given protein are of high interest. One of the main algorithms devised in recent years to quantify thermodynamic properties of water is the grid inhomogeneous solvation theory (GIST), which calculates these features on a grid surrounding the protein. Despite the inherent advantages of GIST, the computational demand is a major drawback, as calculations for larger systems can take days or even weeks. Here, we present a GPU accelerated version of the GIST algorithm, which facilitates efficient estimates of solvation free energy even of large biomolecular interfaces. Furthermore, we show

SUBMITTER: Kraml J 

PROVIDER: S-EPMC7032847 | biostudies-literature | 2019 Nov

REPOSITORIES: biostudies-literature