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BioMed Research International
Volume 2013 (2013), Article ID 409658, 7 pages
An Accurate Method for Prediction of Protein-Ligand Binding Site on Protein Surface Using SVM and Statistical Depth Function
1College of Mathematical Sciences and LPMC, Nankai University, Tianjin 300071, China
2Division of Experimental Cancer, Cross Cancer Institute, 115660 University Avenue, Edmonton, AB, Canada T6G 2V4
Received 17 May 2013; Revised 15 August 2013; Accepted 29 August 2013
Academic Editor: Bing Niu
Copyright © 2013 Kui Wang et al. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
- H. M. Berman, J. Westbrook, Z. Feng et al., “The protein data bank,” Nucleic Acids Research, vol. 28, no. 1, pp. 235–242, 2000.
- D. S. Wishart, C. Knox, A. C. Guo et al., “DrugBank: a knowledgebase for drugs, drug actions and drug targets,” Nucleic Acids Research, vol. 36, no. 1, pp. D901–D906, 2008.
- A. H. Elcock, “Prediction of functionally important residues based solely on the computed energetics of protein structure,” Journal of Molecular Biology, vol. 312, no. 4, pp. 885–896, 2001.
- P. Bate and J. Warwicker, “Enzyme/non-enzyme discrimination and prediction of enzyme active site location using charge-based methods,” Journal of Molecular Biology, vol. 340, no. 2, pp. 263–276, 2004.
- J. An, M. Totrov, and R. Abagyan, “Pocketome via comprehensive identification and classification of ligand binding envelopes,” Molecular and Cellular Proteomics, vol. 4, no. 6, pp. 752–761, 2005.
- A. T. R. Laurie and R. M. Jackson, “Q-SiteFinder: an energy-based method for the prediction of protein-ligand binding sites,” Bioinformatics, vol. 21, no. 9, pp. 1908–1916, 2005.
- D. G. Levitt and L. J. Banaszak, “POCKET: a computer graphics method for identifying and displaying protein cavities and their surrounding amino acids,” Journal of Molecular Graphics, vol. 10, no. 4, pp. 229–234, 1992.
- M. Hendlich, F. Rippmann, and G. Barnickel, “LIGSITE: automatic and efficient detection of potential small molecule-binding sites in proteins,” Journal of Molecular Graphics and Modelling, vol. 15, no. 6, pp. 359–363, 1997.
- R. A. Laskowski, “SURFNET: a program for visualizing molecular surfaces, cavities, and intermolecular interactions,” Journal of Molecular Graphics, vol. 13, no. 5, pp. 323–330, 1995.
- G. P. Brady Jr. and P. F. W. Stouten, “Fast prediction and visualization of protein binding pockets with PASS,” Journal of Computer-Aided Molecular Design, vol. 14, no. 4, pp. 383–401, 2000.
- T. A. Binkowski, S. Naghibzadeh, and J. Liang, “CASTp: computed atlas of surface topography of proteins,” Nucleic Acids Research, vol. 31, no. 13, pp. 3352–3355, 2003.
- H. Edelsbrunner and E. Mucke, “Three-dimensional alpha shapes,” ACM Transactions on Graphics, vol. 13, pp. 43–72, 1994.
- B. Huang and M. Schroeder, “LIGSITEcsc: predicting ligand binding sites using the connolly surface and degree of conservation,” BMC Structural Biology, vol. 6, article 19, 2006.
- M. Landau, I. Mayrose, Y. Rosenberg et al., “ConSurf 2005: the projection of evolutionary conservation scores of residues on protein structures,” Nucleic Acids Research, vol. 33, no. 2, pp. W299–W302, 2005.
- J. A. Capra, R. A. Laskowski, J. M. Thornton, M. Singh, and T. A. Funkhouser, “Predicting protein ligand binding sites by combining evolutionary sequence conservation and 3D structure,” PLoS Computational Biology, vol. 5, no. 12, Article ID e1000585, 2009.
- T. Zhang, H. Zhang, K. Chen, S. Shen, J. Ruan, and L. Kurgan, “Accurate sequence-based prediction of catalytic residues,” Bioinformatics, vol. 24, no. 20, pp. 2329–2338, 2008.
- H. R. Ansari and G. P. S. Raghava, “Identification of NAD interacting residues in proteins,” BMC Bioinformatics, vol. 11, article 160, 2010.
- C.-W. Cheng, E. C.-Y. Su, J.-K. Hwang, T.-Y. Sung, and W.-L. Hsu, “Predicting RNA-binding sites of proteins using support vector machines and evolutionary information,” BMC Bioinformatics, vol. 9, supplement 12, article S6, 2008.
- Y. Ofran and B. Rost, “ISIS: interaction sites identified from sequence,” Bioinformatics, vol. 23, no. 2, pp. e13–e16, 2007.
- R. Wang, X. Fang, Y. Lu, C.-Y. Yang, and S. Wang, “The PDBbind database: methodologies and updates,” Journal of Medicinal Chemistry, vol. 48, no. 12, pp. 4111–4119, 2005.
- J. W. Tukey, “Mathematics and picturing data,” in In Proceedings of International Congress of Mathematicians, vol. 2, pp. 523–531, Vancouver, Canada, 1975.
- W. Kabsch and C. Sander, “Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features,” Biopolymers, vol. 22, no. 12, pp. 2577–2637, 1983.
- S. Kawashima, P. Pokarowski, M. Pokarowska, A. Kolinski, T. Katayama, and M. Kanehisa, “AAindex: amino acid index database, progress report 2008,” Nucleic Acids Research, vol. 36, no. 1, pp. D202–D205, 2008.
- S. Sarkhel and G. R. Desiraju, “N–H…O, O–H…O, and C–H…O hydrogen bonds in protein-ligand complexes: strong and weak interactions in molecular recognition,” Proteins, vol. 54, no. 2, pp. 247–259, 2004.
- S. F. Altschul, T. L. Madden, A. A. Schäffer et al., “Gapped BLAST and PSI-BLAST: a new generation of protein database search programs,” Nucleic Acids Research, vol. 25, no. 17, pp. 3389–3402, 1997.
- C.-C. Chang and C.-J. Lin, “LIBSVM: a library for support vector machines,” 2001, http://www.csie.ntu.edu.tw/~cjlin/libsvm/.