Ontology highlight
ABSTRACT:
SUBMITTER: Cao X
PROVIDER: S-EPMC10836080 | biostudies-literature | 2024 Jan
REPOSITORIES: biostudies-literature
Cao Xin X Hummel Michelle H MH Wang Yuzhang Y Simmerling Carlos C Coutsias Evangelos A EA
ArXiv 20240425
In this paper, we present dSASA (differentiable SASA), an exact geometric method to calculate solvent accessible surface area (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 tetrahedrization adapted for efficient GPU implementation and the SASA values for atoms and molecules are calculated based on the tetrahedrization information and inclusion-exclusion method. The SASA values from the numeri ...[more]