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BioMed Research International
Volume 2013 (2013), Article ID 409658, 7 pages
http://dx.doi.org/10.1155/2013/409658
Research Article

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.

Linked References

  1. H. M. Berman, J. Westbrook, Z. Feng et al., “The protein data bank,” Nucleic Acids Research, vol. 28, no. 1, pp. 235–242, 2000. View at Scopus
  2. 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. View at Publisher · View at Google Scholar · View at Scopus
  3. 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. View at Publisher · View at Google Scholar · View at Scopus
  4. 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. View at Publisher · View at Google Scholar · View at Scopus
  5. 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. View at Publisher · View at Google Scholar · View at Scopus
  6. 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. View at Publisher · View at Google Scholar · View at Scopus
  7. 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. View at Publisher · View at Google Scholar · View at Scopus
  8. 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. View at Publisher · View at Google Scholar · View at Scopus
  9. 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. View at Publisher · View at Google Scholar · View at Scopus
  10. 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. View at Publisher · View at Google Scholar · View at Scopus
  11. 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. View at Publisher · View at Google Scholar · View at Scopus
  12. H. Edelsbrunner and E. Mucke, “Three-dimensional alpha shapes,” ACM Transactions on Graphics, vol. 13, pp. 43–72, 1994.
  13. 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. View at Publisher · View at Google Scholar · View at Scopus
  14. 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. View at Publisher · View at Google Scholar · View at Scopus
  15. 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. View at Publisher · View at Google Scholar · View at Scopus
  16. 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. View at Publisher · View at Google Scholar · View at Scopus
  17. H. R. Ansari and G. P. S. Raghava, “Identification of NAD interacting residues in proteins,” BMC Bioinformatics, vol. 11, article 160, 2010. View at Publisher · View at Google Scholar · View at Scopus
  18. 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. View at Publisher · View at Google Scholar · View at Scopus
  19. Y. Ofran and B. Rost, “ISIS: interaction sites identified from sequence,” Bioinformatics, vol. 23, no. 2, pp. e13–e16, 2007. View at Publisher · View at Google Scholar · View at Scopus
  20. 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. View at Publisher · View at Google Scholar · View at Scopus
  21. J. W. Tukey, “Mathematics and picturing data,” in In Proceedings of International Congress of Mathematicians, vol. 2, pp. 523–531, Vancouver, Canada, 1975.
  22. 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. View at Scopus
  23. 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. View at Publisher · View at Google Scholar · View at Scopus
  24. 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. View at Publisher · View at Google Scholar · View at Scopus
  25. 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. View at Publisher · View at Google Scholar · View at Scopus
  26. C.-C. Chang and C.-J. Lin, “LIBSVM: a library for support vector machines,” 2001, http://www.csie.ntu.edu.tw/~cjlin/libsvm/.