| Parameter selection of pocket extraction algorithm using interaction interface |
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| 作者姓名： | KIM Chong-Min WON Chung-In RYU Joonghyun CHO Cheol-Hyung BHAK Jonghwa KIM Deok-Soo |
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| 作者单位： | Department of Industrial Engineering Hanyang University Seoul 133-791 Korea，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) |
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| 基金项目： | Project supported by Creative Research Initiative from the Ministry of Science and Technology (MOST), Korea. BHAK Jonghwa is supported by Biogreen21 Fund and MOST Funds, Korea |
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| 摘 要： | INTRODUCTION Being the bio era, a significant research effort has been devoted to the study of proteins since they are related to the critical body functions. There have been many studies on proteins, with the voluminous related data being currently available in various pub- lic repositories including the Protein Data Bank (PDB) (CATH, 2006; DALI, 2006; MSD, 2006; RCSB PDB, 2006; SCOP Database, 2006). Given the atomic complexes of proteins, ana- lyzing interactions between them…
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| 关 键 词： | 蛋白质 交互作用 沃罗诺框图 参数选择 算法 |
| 收稿时间： | 2006-05-20 |
| 修稿时间： | 2006-06-21 |
Parameter selection of pocket extraction algorithm using interaction interface |
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| KIM Chong-Min WON Chung-In RYU Joonghyun CHO Cheol-Hyung BHAK Jonghwa KIM Deok-Soo.Parameter selection of pocket extraction algorithm using interaction interface[J].Journal of Zhejiang University Science,2006,7(9):1492-1499. |
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| Authors: | Chong-Min Kim Chung-In Won Joonghyun Ryu Cheol-Hyung Cho Jonghwa Bhak Deok-Soo Kim |
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| Institution: | (1) Department of Industrial Engineering, Hanyang University, Seoul, 133-791, Korea;(2) Voronoi Diagram Research Center, Hanyang University, Seoul, 133-791, Korea;(3) Samsung Electronics, Suwon, Gyeonggi-do, 443-742, Korea;(4) Korean Bioinformation Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, 305-806, Korea |
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| Abstract: | 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. |
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| Keywords: | Pocket Protein Interaction interface Protein interaction Voronoi diagram |
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