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ZJUS-A
Journal of Zhejiang University-SCIENCE A (Applied Physics & Engineering)  2006, Vol. 7 Issue ( 9): 5-    DOI: 10.1631/jzus.2006.A1492
    
Parameter selection of pocket extraction algorithm using interaction interface
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
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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.

Key words： Pocket      Protein      Interaction interface      Protein interaction      Voronoi diagram     
Received: 20 May 2006     
CLC:  TP393  
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KIM Chong-Min
WON Chung-In
RYU Joonghyun
CHO Cheol-Hyung
BHAK Jonghwa
KIM Deok-Soo
Cite this article:

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. Journal of Zhejiang University-SCIENCE A (Applied Physics & Engineering), 2006, 7( 9): 5-.

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http://www.zjujournals.com/xueshu/zjus-a/10.1631/jzus.2006.A1492     OR     http://www.zjujournals.com/xueshu/zjus-a/Y2006/V7/I 9/5

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