An Algorithm for Finding Surface Atoms of a Protein Molecule Based on Voxel Map Representation


The KIPS Transactions:PartA, Vol. 19, No. 2, pp. 73-76, Apr. 2012
10.3745/KIPSTA.2012.19.2.73,   PDF Download:

Abstract

In this paper, we propose an efficient method to extract surface atoms from a protein molecule. Surface atoms are defined as a set of atoms who can contact given probe solvent P, where P does not collide with the molecule. The atoms contained in the molecule are represented as a set of spheres with van der Waals radii. The probe solvent also is represented as a sphere. We propose a method to extract the surface atoms by computing the offset surface of the molecule with respect to the radius of P. For efficient computation of the offset surface of a molecule, a voxel map is constructed for the offset surfaces of the spheres. Based on GPU (graphic processor unit) acceleration, a data parallel algorithm is used to extract the surface atoms in 42.87 milliseconds for the molecule containing up to 6,412 atoms.


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Cite this article
[IEEE Style]
B. J. Kim, K. J. Kim, J. K. Seong, "An Algorithm for Finding Surface Atoms of a Protein Molecule Based on Voxel Map Representation," The KIPS Transactions:PartA, vol. 19, no. 2, pp. 73-76, 2012. DOI: 10.3745/KIPSTA.2012.19.2.73.

[ACM Style]
Byung Joo Kim, Ku Jin Kim, and Joon Kyung Seong. 2012. An Algorithm for Finding Surface Atoms of a Protein Molecule Based on Voxel Map Representation. The KIPS Transactions:PartA, 19, 2, (2012), 73-76. DOI: 10.3745/KIPSTA.2012.19.2.73.