Divide-and-conquer strategy for large-scale Eulerian solvent excluded surface.

ABSTRACT:

Motivation

Surface generation and visualization are some of the most important tasks in biomolecular modeling and computation. Eulerian solvent excluded surface (ESES) software provides analytical solvent excluded surface (SES) in the Cartesian grid, which is necessary for simulating many biomolecular electrostatic and ion channel models. However, large biomolecules and/or fine grid resolutions give rise to excessively large memory requirements in ESES construction. We introduce an out-of-core and parallel algorithm to improve the ESES software.

Results

The present approach drastically improves the spatial and temporal efficiency of ESES. The memory footprint and time complexity are analyzed and empirically verified through extensive tests with a large collection of biomolec

SUBMITTER: Zhao R 

PROVIDER: S-EPMC6641554 | biostudies-literature | 2018

REPOSITORIES: biostudies-literature