Exact Analytical Algorithm for the Solvent-Accessible Surface Area and Derivatives in Implicit Solvent Molecular Simulations on GPUs.

ABSTRACT: In this paper, we present differentiable solvent-accessible surface area (dSASA), an exact geometric method to calculate SASA analytically along with atomic derivatives on GPUs. The atoms in a molecule are first assigned to tetrahedra in groups of four atoms by Delaunay tetrahedralization adapted for efficient GPU implementation, and the SASA values for atoms and molecules are calculated based on the tetrahedralization information and inclusion-exclusion method. The SASA values from the numerical icosahedral-based method can be reproduced with >98% accuracy for both proteins and RNAs. Having been implemented on GPUs and incorporated into AMBER, we can apply dSASA to implicit solvent molecular dynamics simulations with the inclusion of this nonpolar term. The current GPU version of GB/SA si

SUBMITTER: Cao X 

PROVIDER: S-EPMC11530138 | biostudies-literature | 2024 Jun

REPOSITORIES: biostudies-literature