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Connolly Surface on an Atomic Structure via Voronoi Diagram of Atoms

Journal of Computer Science & Technology 2006年第2期21卷 255-260页

作者： joonghyun ryu Rhohun Park Deok-Soo Kim Voronoi Diagram Research Center Hanyang University Seoul Korea Department of Industrial Engineering Hanyang University Seoul Korea

One of the most important geometric structures of a protein is the Connolly surface of protein since a Connolly surface plays an important role in protein folding, docking, interactions between proteins, amongst other things. This paper presents an algorithm for precisely and efficiently computing the Connolly surface of a protein using a proposed geometric construct called β-shape based on the Voronoi diagram of atoms in the protein. Given the Voronoi diagram of atoms based on the Euclidean distance from the atom surfaces, the proposed algorithm first computes a β-shape with an appropriate probe. Then, the Connolly surface is computed by employing the blending operation on the atomic complex of the protein by the given probe.

关键词： protein Connolly/molecular surface β-shape Voronoi diagram of atoms blending surface

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Parameter selection of pocket extraction algorithm using interaction interface

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Journal of Zhejiang University-Science A(Applied Physics & Engineering) 2006年第9期7卷 1492-1499页

作者： KIM Chong-Min WON Chung-In ryu joonghyun CHO Cheol-Hyung BHAK Jonghwa KIM Deok-Soo Department of Industrial Engineering Hanyang University Seoul 133-791 Korea Voronoi Diagram Research Center Hanyang University Seoul 133-791 Korea Samsung Electronics Suwon Gyeonggi-do 443-742 Korea Korean Bioinformation Center Korea Research Institute of Bioscience and Biotechnology Daejeon 305-806 Korea Department of Industrial Engineering Hanyang University Seoul 133-791 Korea)

Pockets in proteins have been known to be very important for the life process. There have been several studies in the past to automatically extract the pockets from the structure information of known proteins. However, it is difficult to find a study comparing the precision of the extracted pockets from known pockets on the protein. In this paper, we propose an algorithm for extracting pockets from structure data of proteins and analyze the quality of the algorithm by comparing the extracted pockets with some known pockets. These results in this paper can be used to set the parameter values of the pocket extraction algorithm for getting better results.

关键词： Pocket Protein Interaction interface Protein interaction Voronoi diagram

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