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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.

[1] Agarwal, P.K., Edelsbrunner, H., Harer, J., Wang, Y., 2004. Extreme Elevation on a 2-manifold. Proc. of the 20th Annual ACM Symposium on Computational Geometry, Brooklyn, New York, USA, p.357-365.

[2] Ban, Y.E.A., Edelsbrunner, H., Rudolph, J., 2004. Interface Surfaces for Protein-protein Complexes. Proc. of the 8th Annual International Conference on Research in Computational Molecular Biology, San Diego, CA, p.205-212.

[3] Berg, J.M., Tymoczko, J.L., Stryer, L., 2002. Biochemistry (5th Ed.). W.H. Freeman.

[4] Bilder, P.W., Ding, H., Newcomer, M.E., 2004. Crystal structure of the ancient, Fe-S scafold IscA reveals a novel protein fold. Biochemistry, 43(1):133-139.

[5] Bourne, P.E., Weissig, H., 2003. Structural Bioinformatics. Wiley-Liss.

[6] CATH Database, 2006. Http://www.biochem.ucl.ac.uk/bsm/ cath/.

[7] Creighton, T.E., 1999. Protein Folding. W.H. Freeman.

[8] DALI Domain Dictionary, 2006. Http://www.ebi.ac.uk/dali/ domain/.

[9] Edelsbrunner, H., Facello, M., Liang, J., 1998. On the definition and the construction of pockets in macromolecules. Discrete Applied Mathematics, 88(1-3):83-102.

[10] Heifetz, A., Eisenstein, M., 2003. Effect of local shape modifications of molecular surfaces on rigid-body protein-protein docking. Protein Engineering, 16(3):179-185.

[11] Jones, S., Thornton, J.M., 1996. Principles of Protein-protein Interactions. Proc. of the National Academy of Sciences of the United States of America, 93(1):13-20.

[12] Kim, C.M., 2005. Interaction Interfaces in Proteins Using Voronoi Diagram of Atoms and Their Database. Master’s Thesis, Hanyang University, Korea.

[13] Kim, D.S., 2004. Euclidean Voronoi Diagram of Atoms and Protein. Proc. of the 1st BioGeometry Meeting—In Conjunction with the ACM Symposium on Computational Geometry. The Technical University of New York, New York, USA.

[14] Kim, D.S., Cho, Y., Kim, D., 2004a. Edge-tracing Algorithm for Euclidean Voronoi Diagram of 3D Spheres. Proc. of the 16th Canadian Conference on Computational Geometry, p.176-179.

[15] Kim, D.S., Cho, Y., Kim, D., Cho, C.H., 2004b. Protein Structure Analysis Using Euclidean Voronoi Diagram of Atoms. Proc. of the International Workshop on Biometric Technologies (BT2004), p.125-129.

[16] Kim, D.S., Cho, Y., Kim, D., Kim, S., Bhak, J., Lee, S.H., 2004c. Euclidean Voronoi Diagrams of 3D Spheres and Applications to Protein Structure Analysis. Proc. of the 1st International Symposium on Voronoi Diagrams in Science and Engineering (VD2004), p.137-144.

[17] Kim, D.S., Cho, C.H., Ryu, J., Kim, D., 2005a. Three dimensional beta shapes (Submitted to Computer-Aided Design).

[18] Kim, D.S., Cho, Y., Kim, D., 2005b. Euclidean Voronoi diagram of 3D balls and its computation via tracing edges. Computer-Aided Design, 37(13):1412-1424.

[19] Kim, D.S., Cho, Y., Kim, D., Kim, S., Bhak, J., Lee, S.H., 2005c. Euclidean Voronoi diagrams of 3D spheres and applications to protein structure analysis. Japan Journal of Industrial and Applied Mathematics, 22(2):251-265.

[20] Kim, D.S., Cho, C.H., Kim, D., Cho, Y., 2006. Recognition of docking sites on a protein using β-shape based on Voronoi diagram of atoms. Computer-Aided Design, 38(5):431-443.

[21] Kuntz, I.D., 1992. Structure-based strategies for drug design and discovery. Science, 257(21):1078-1082.

[22] Lee, B., Richard, F.M., 1971. The interpretation of protein structures: Estimation of static accessibility. Journal of Molecular Biology, 55(3):379-400.

[23] Liang, J., Edelsbrunner, H., Woodward, C., 1998. Anatomy of protein pockets and cavities: Measurement of binding site geometry and implications for ligand design. Protein Science, 7:1884-1897.

[24] MSD (Macromolecular Structure Database), 2005. Http://www.ebi.ac.uk/msd/.

[25] Nooren, I.M.A., Thornton, J.M., 2003. Diversity of protein-protein interactions. The EMBO Journal, 22(14):3486-3492.

[26] Ofran, Y., Rost, B., 2003. Analysing six types of protein-protein interfaces. Journal of Molecular Biology, 325(2):377-387.

[27] Parsons, D., Canny, J., 1994. Geometric Problems in Molecular Biology. Proc. of the 2nd International Conference on Intelligent Systems for Molecular Biology. Stanford University, California, USA, p.322-330.

[28] Peters, K.P., Fauck, J., Frommel, C., 1996. The automatic search for ligand binding sites in protein of known three dimensional structure using only geometric criteria. Journal of Molecular Biology, 256(1):201-213.

[29] RCSB PDB, 2006. Protein Data Bank Homepage. Http://www.rcsb.org/pdb/.

[30] SCOP Database, 2006. Http://scop.berkeley.edu/.

[31] Sheinerman, F.B., Honig, B., 2002. On the role of electrostatic interactions in the design of protein-protein interfaces. Journal of Molecular Biology, 318(1):161-177.

[32] Shoichet, B., Kunts, I., 1991. Protein docking and complementarity. Journal of Molecular Biology, 221(1):327-346.

[33] Tsai, C.J., Lin, S.L., Wolfon, H.J., Nussinov, R., 1997. Studies of protein-protein interfaces: A statistical analysis of the hydrophobic effect. Protein Science, 6:53-54.

[34] Varshney, A., Brooks, F.P.Jr., Richardson, D.C., Wright, W.V., Manocha, D., 1995. Defining, Computing, and Visualizing Molecular Interfaces. Proc. of the IEEE Visualization ’95, Atlanta, GA, p.36-43.

[35] Xu, D., Tsai, C.J., Nussinov, R., 1997. Hydrogen bonds and salt bridges across protein-protein interfaces. Protein Engineering, 10(9):999-1012.