GPU Accelerated Finding of Channels and Tunnels for a Protein Molecule
- 주제(키워드) Cavities , Channels , GPU programming , Protein molecules , Tunnels
- 관리정보기술 faculty
- 등재 SCIE, SCOPUS
- 발행기관 Springer New York LLC
- 발행년도 2014
- 총서유형 Journal
- URI http://www.dcollection.net/handler/ewha/000000110511
- 본문언어 영어
- Published As http://dx.doi.org/10.1007/s10766-014-0331-8
초록/요약
This paper proposes a novel method for computing the cavities and channels/tunnels in a protein molecule in interactive time without significant user effort. A sphere tree structure is used to represent a protein molecule, which provides a parallel architecture to access a Graphic Processing Unit (GPU) memory. The use of CUDA programming with a GPU then allows the proposed system to work in parallel on either a sphere tree structure of a molecule or a set of voxels composing the space. A real-time performance is achieved for proximity queries on a protein molecule, and an interactive time performance is realized for finding all the cavities and channel/tunnels without user effort. The proposed system also provides a method for approximating a convex hull of a molecule in a discrete space, and then generates the shortest path from a user selected or automatically chosen cavity to the exterior of the protein molecule. Experimental results in comparison with previous methods confirm the time efficiency of the proposed system.
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