Browse > Article
http://dx.doi.org/10.3745/KIPSTA.2012.19A.4.169

Voronoi Diagram Computation for a Molecule Using Graphics Hardware  

Lee, Jung-Eun (경북대학교 전자전기컴퓨터학부)
Baek, Nak-Hoon (경북대학교 컴퓨터학부)
Kim, Ku-Jin (경북대학교 컴퓨터학부)
Publication Information
The KIPS Transactions:PartA / v.19A, no.4, 2012 , pp. 169-174 More about this Journal
Abstract
We present an algorithm that computes a 3 dimensional Voronoi diagram for a protein molecule in this paper. The molecule is represented as a set of spheres with van der Waals radii. The Voronoi diagram is constructed in the 3D space by finding the voxels containing it. For the feasibility of the computation, we represent the molecule as a BVH (bounding volume hierarchy), and our system is accelerated by modern graphics hardware with CUDA programming support. Compared to single-core CPU implementations, experimental results show 323 times faster performance in the computation time, when the space is partitioned into $2^{24}$ voxels.
Keywords
Voronoi Diagram; GPU; Protein Molecule;
Citations & Related Records
연도 인용수 순위
  • Reference
1 N. Ray, X. Cavin, J. -C. Paul and B. Maigret, "Intersurf: dynamic interface between proteins", Journal of Molecular Graphics and Modelling, Vol.23, No.4, pp.347-354, 2005.   DOI   ScienceOn
2 F. Richards, "The interpretation of protein structures: total volume, group volume distributions and packing density," Journal of Molecular Biology, Vol.82, pp.1-14, 1974.   DOI
3 G. Rong and T. -S. Tan, "Variants of jump flooding algorithm for computing discrete Voronoi diagrams," Proceedings of the 4thInternational Symposium on Voronoi Diagrams in Science and Engineering, pp.176-181, 2007.
4 A. Varshney, F. P. Brooks, D. C. Richardson, W. V. Wright and D. Manocha, "Defining, computing, and visualizing molecular interfaces," Proceedings of the IEEE visualization, pp.36-43, 1995.
5 C. -M. Kim, C. -I. Won, Y. Cho, D. Kim, S. Lee, J. Bhak and D. -S. Kim, "Interaction interfaces in proteins via the Voronoi diagram of atoms," Computer-Aided Design, Vol.38, pp.1192-1204, 2006.   DOI   ScienceOn
6 D. -S. Kim, Y. Cho and D. Kim, "Euclidean Voronoi diagram of 3D balls and its computation via tracing edges," Computer-Aided Design, Vol.37, pp.1412-1424, 2005.   DOI   ScienceOn
7 J. Bernauer, J. Aze, J. Jain and A. Poupon, "A new protein-protein docking scoring function based on interface residue properties," Bioinformatics, Vol.23, No.5, pp.555-562, 2007.   DOI   ScienceOn
8 D. -S. Kim, D. Kim and Y. Cho, "Euclidean voronoi diagrams of 3D spheres: Their construction and related problems from biochemistry," Mathematics of Surfaces 2005, LNCS 3604, pp.255-271, 2005.
9 K. -J. Kim, J. -E. Lee, N. Baek, "Voronoi diagram computation for protein molecules using graphics hardware (poster)," Proceedings of ACM SIGGRAPH, 2010.
10 A. Poupon, "Voronoi and Voronoi-related tessellations in studies of protein structure and interaction," Current Opinion in Structural Biology, Vol.14, No.2, pp.233-241, 2004.   DOI   ScienceOn
11 A. Bondi, "van der Waals Volumes and Radii," The Journal of Physical Chemistry, Vol.68, No.3, pp.441-451, 1964.   DOI
12 I. Fischer and C. Gotsman, "Fast Approximation of High-Order Voronoi Diagrams and Distance Transforms on the GPU," Journal of Graphics Tools, Vol.11, No.4, pp.39-60, 2006.   DOI
13 Y. -E. A. Ban, H. Edelsbrunner and J. Rudolph, "Interface surfaces for protein-protein complexes," Proceedings of the 8th annual international conference on research in computational molecular biology, pp.205-212, 2004.
14 M. Gerstein and F. M. Richards, "Protein Geometry: Distances, Areas, and Volumes," International Tables for Crystallography (Rossmann, M. and Arnold, E., eds.), Vol. F: Crystallography of biological macromolecules, pp.531-539, 2001.
15 K. E. Hoff III, J. Keyser, M. Lin, D. Manocha and T. Culver, "Fast computation of generalized Voronoi diagrams using graphics hardware," SIGGRAPH'99 Proc. of the 26th annual conference on Computer graphics and interactive techniques, pp.277-286, 1999.
16 H. -H. Hsieh and W. -K. Tai, "A simple GPU-based approach for 3D Voronoi diagram construction and visualization," Simulation Modelling Practice and Theory, Vol.13, pp.681-692, 2005.   DOI   ScienceOn