GPU accelerated molecular surface computing

Byungjoo Kim, Ku Jin Kim, Jun Kyung Seong

Research output: Contribution to journalArticle

9 Citations (Scopus)

Abstract

A method is presented for computing the SES (solvent excluded surface) of a protein molecule in interactive-time based on GPU (graphics processing unit) acceleration. First, the offset surface of the van der Waals spheres is sampled using an offset distance d that corresponds to the radius of the solvent probe. The SES is then constructed by extracting the surface at distance d from the sample points. For interactive-time computing, two space partitioning schemes are used, a voxel map and kd-tree, with data parallel schemes accelerated by GPU. In experiments using an average 1,848 atoms, a SES with a resolution of 1/27×1/27×1/27 of the original bounding box is obtained in 66.53ms on average.

Original languageEnglish
JournalApplied Mathematics and Information Sciences
Volume6
Issue number1 SUPPL.
Publication statusPublished - 2012 Jan 1
Externally publishedYes

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Keywords

  • GPU acceleration
  • Molecular surface
  • Offset
  • Solvent-excluded surface
  • Voxel map

ASJC Scopus subject areas

  • Applied Mathematics
  • Numerical Analysis
  • Analysis
  • Computer Science Applications
  • Computational Theory and Mathematics

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