Finding surface atoms of a protein molecule on a GPU

Byungjoo Kim, Ku Jin Kim, Ji Hoon Choi, Nakhoon Baek, Joon Kyung Seong, Yoo Joo Choi

Research output: Chapter in Book/Report/Conference proceedingConference contribution

3 Citations (Scopus)


We present a real-time method to find the atoms at the boundary surface of a protein molecule. Efficient finding of the atoms at the surface of the molecule is important since most of interactions between two protein molecules including docking and binding occur at the boundary surface of molecules. [Deanda, et al. 2002] proposed a method to extract surface atoms based on solvent-accessible surfaces. Solvent-accessible surface is a trajectory of the center of probe solvent, where the solvent touches the molecule without interference. They defined surface atoms as the atoms that touch the solvent probes. We represent the protein molecule as a set of spheres with van der Waals radii: M = {S(c i, r i)}, where S(c i, r i) is a sphere with center point c i and radius r i. The probe solvent is represented as a sphere with radius d. We compute the offset surface of M with offset distance d. Then, we find the spheres in M, whose d-offset surface has an intersection with the d-offset surface of M. To achieve the real-time performance, our algorithm is implemented on a GPU.

Original languageEnglish
Title of host publicationSIGGRAPH Asia 2011 Posters, SA'11
Publication statusPublished - 2011
Externally publishedYes
EventSIGGRAPH Asia 2011 Posters, SA'11 - Hong Kong, China
Duration: 2011 Dec 122011 Dec 15

Publication series

NameSIGGRAPH Asia 2011 Posters, SA'11


OtherSIGGRAPH Asia 2011 Posters, SA'11
CityHong Kong

ASJC Scopus subject areas

  • Computer Graphics and Computer-Aided Design
  • Computer Vision and Pattern Recognition


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