Browse > Article
http://dx.doi.org/10.3745/KIPSTA.2012.19A.2.073

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

Kim, Byung-Joo (경북대학교 전자공학과)
Kim, Ku-Jin (경북대학교 컴퓨터학부)
Seong, Joon-Kyung (숭실대학교 컴퓨터학부)
Publication Information
The KIPS Transactions:PartA / v.19A, no.2, 2012 , pp. 73-76 More about this Journal
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.
Keywords
Protein Molecule; Surface Atom; Molecule Docking; Voxel Map; Offset Surface; GPU;
Citations & Related Records
연도 인용수 순위
  • Reference
1 Connolly, M.L.: Solvent-accessible surfaces of proteins and nucleic acids. Science 221, 709-713, 1983.   DOI
2 Nicholls, A., Sharp, K., Honig, B.: Protein folding and association: insights from the interfacial and thermodynamic properties of hydrocarbons. Proteins 11(4), 281-296, 1991.   DOI   ScienceOn
3 Pettersen, E.F., Goddards, T.D., Huang, C.C., Couch, G.S., Greenblatt, D.M., Meng, E.C., Ferrin, T.E.: Ucsf chimera: a visualization system for exploratory research and analysis. J. Comput. Chem. 25(13), 1605-1612, 2004   DOI   ScienceOn
4 Ryu, J., Park, R., Kim, D.S.: Molecular surfaces on proteins via beta shapes. Computer-Aided Design 39, 1042-1057, 2007.   DOI   ScienceOn
5 Sanner, M.F., Spehner, J.C., Olson, A.J.: Reduced surface: an efficient way to compute molecular surfaces. Biopolymers 38(3), 305-320, 1996.   DOI   ScienceOn
6 Zauhar, R.J.: Smart: a solvent-accessible triangulated surface generator for molecular graphics and boundary element applications. J Comput Aided Mol Des 9(2), 149-159, 1995.   DOI   ScienceOn
7 Deanda, F., Pearlman, R.S.: A novel approach for identifying the surface atoms of macro-molecules. Journal of Molecular Graphics and Modelling 20, 415-425, 2002.   DOI   ScienceOn
8 http://www.pdb.org
9 Can, T., Chen, C.I., Wang, Y.F.: Efficient molecular surface generation using level-set methods. J. of Molecular Graphics and Modeling 25(4), 442-454, 2006.   DOI   ScienceOn
10 Connolly, M.L.: Analytical molecular surface calculation. J. Appl. Crystallogr. pp.548-558, 1983.