Table of Contents Author Guidelines Submit a Manuscript
International Journal of Biomedical Imaging
Volume 2011 (2011), Article ID 918978, 15 pages
http://dx.doi.org/10.1155/2011/918978
Research Article

Protein Surface Characterization Using an Invariant Descriptor

1Lane Department of Computer Science and Electrical Engineering, West Virginia University, Morgantown, WV 26506, USA
2Department of Pathology, Anatomy and Cell Biology Jefferson Medical College, Thomas Jefferson University, Philadelphia, PA 19107, USA

Received 6 July 2011; Accepted 14 August 2011

Academic Editor: Guowei Wei

Copyright © 2011 Zainab Abu Deeb 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. L. Jaroszewski, Z. Li, S. S. Krishna et al., “Exploration of uncharted regions of the protein universe,” PLoS Biology, vol. 7, no. 9, Article ID e1000205, 2009. View at Publisher · View at Google Scholar · View at Scopus
  2. Y. T. Yan and W. H. Li, “Identification of protein functional surfaces by the concept of a split pocket,” Proteins, vol. 76, no. 4, pp. 959–976, 2009. View at Publisher · View at Google Scholar · View at Scopus
  3. Y. Loewenstein, D. Raimondo, O. C. Redfern et al., “Protein function annotation by homology-based inference,” Genome Biology, vol. 10, no. 2, pp. 207.1–207.8, 2009. View at Google Scholar · View at Scopus
  4. S. Sivashankari and P. Shanmughavel, “Functional annotation of hypothetical proteins—a review,” Bioinformation, vol. 1, no. 8, pp. 335–338, 2006. View at Google Scholar
  5. F. Ferrè, G. Ausiello, A. Zanzoni, and M. Helmer-Citterich, “SURFACE: a database of protein surface regions for functional annotation,” Nucleic Acids Research, vol. 32, pp. D240–D244, 2004. View at Google Scholar · View at Scopus
  6. D. Gront, A. Kolinski, and U. H. E. Hansmann, “Protein structure prediction by tempering spatial constraints,” Journal of Computer-Aided Molecular Design, vol. 19, no. 8, pp. 603–608, 2005. View at Publisher · View at Google Scholar · View at Scopus
  7. L. Sael, B. Li, D. La et al., “Fast protein tertiary structure retrieval based on global surface shape similarity,” Proteins: Structure, Function, and Bioinformatics, vol. 72, no. 4, pp. 1259–1273, 2008. View at Publisher · View at Google Scholar · View at Scopus
  8. S. Yin, E. A. Proctor, A. A. Lugovskoy, and N. V. Dokholyan, “Fast screening of protein surfaces using geometric invariant fingerprints,” Proceedings of the National Academy of Sciences of the United States of America, vol. 106, no. 39, pp. 16622–16626, 2009. View at Publisher · View at Google Scholar · View at Scopus
  9. N. Nagano, C. A. Orengo, and J. M. Thornton, “One fold with many functions: the evolutionary relationships between TIM barrel families based on their sequences, structures and functions,” Journal of Molecular Biology, vol. 321, no. 5, pp. 741–765, 2002. View at Publisher · View at Google Scholar · View at Scopus
  10. H. H. Gan, R. A. Perlow, S. Roy et al., “Analysis of protein sequence/structure similarity relationships,” Biophysical Journal, vol. 83, no. 5, pp. 2781–2791, 2002. View at Google Scholar · View at Scopus
  11. T. A. Binkowski and A. Joachimiak, “Protein functional surfaces: global shape matching and local spatial alignments of ligand binding sites,” BMC Structural Biology, vol. 8, article 45, 2008. View at Publisher · View at Google Scholar · View at Scopus
  12. A. Godzik, “The structural alignment between two proteins: is there a unique answer?” Protein Science, vol. 5, no. 7, pp. 1325–1338, 1996. View at Google Scholar · View at Scopus
  13. L. K. Buehler and H. H. Rashidi, Bioinformatics Basics: Applications in Biological Science and Medicine, CRC Press, 2005.
  14. D. E. Krane and M. L. Raymer, Fundamental Concepts of Bioinformatics, Pearson Education, 2003.
  15. D. Whitford, Proteins: Structure and Function, John Wiley & Sons, West Sussex, UK, 2005.
  16. M. F. Sanner, A. J. Olson, and J. C. Spehner, “Reduced surface: an efficient way to compute molecular surfaces,” Biopolymers, vol. 38, no. 3, pp. 305–320, 1996. View at Google Scholar · View at Scopus
  17. C. Orengo, D. Jones, and J. Thornton, Bioinformatics Genes, Proteins, and Computers, BIOS Scientific, New York, NY, USA, 2003.
  18. C. Gibas and P. Jambeck, Developing Bioinformatics Computer Skills, O'Reilly Media, Sebastopol, Calif, USA, 2001.
  19. M. L. Connolly, “Shape distributions of protein topography,” Biopolymers, vol. 32, no. 9, pp. 1215–1236, 1992. View at Google Scholar · View at Scopus
  20. P. Rogen and B. Faint, “Automatic classification of protein structure by using Gauss integrals,” Proceedings of the National Academy of Sciences of the United States of America, vol. 100, no. 1, pp. 119–124, 2003. View at Publisher · View at Google Scholar · View at Scopus
  21. M. J. Bayley, E. J. Gardiner, P. Willett, and P. J. Artymiuk, “A fourier fingerprint-based method for protein surface representation,” Journal of Chemical Information and Modeling, vol. 45, no. 3, pp. 696–707, 2005. View at Publisher · View at Google Scholar · View at Scopus
  22. R. J. Morris, R. J. Najmanovich, A. Kahraman, and J. M. Thornton, “Real spherical harmonic expansion coefficients as 3D shape descriptors for protein binding pocket and ligand comparisons,” Bioinformatics, vol. 21, no. 10, pp. 2347–2355, 2005. View at Publisher · View at Google Scholar · View at Scopus
  23. V. Venkatraman, L. Sael, and D. Kihara, “Potential for protein surface shape analysis using spherical harmonics and 3d zernike descriptors,” Cell Biochemistry and Biophysics, vol. 54, no. 1–3, pp. 23–32, 2009. View at Publisher · View at Google Scholar · View at Scopus
  24. L. P. Albou, B. Schwarz, O. Poch, J. M. Wurtz, and D. Moras, “Defining and characterizing protein surface using alpha shapes,” Proteins, vol. 76, no. 1, pp. 1–12, 2009. View at Publisher · View at Google Scholar · View at Scopus
  25. J. Gramm, “A polynomial-time algorithm for the matching of crossing contact-map patterns,” IEEE/ACM Transactions on Computational Biology and Bioinformatics, vol. 1, no. 4, pp. 171–180, 2004. View at Publisher · View at Google Scholar · View at Scopus
  26. K. Lasker, O. Dror, M. Shatsky, R. Nussinov, and H. J. Wolfson, “EMatch: discovery of high resolution structural homologues of protein domains in intermediate resolution Cryo-EM maps,” IEEE/ACM Transactions on Computational Biology and Bioinformatics, vol. 4, no. 1, pp. 28–39, 2007. View at Publisher · View at Google Scholar · View at Scopus
  27. K. Park and D. Kim, “Binding similarity network of ligand,” Proteins, vol. 71, no. 2, pp. 960–971, 2007. View at Google Scholar
  28. L. Sael and D. Kihara, “Improved protein surface comparison and application to low-resolution protein structure data,” BMC Bioinformatics, vol. 11, no. 11, article S2, 2010. View at Publisher · View at Google Scholar · View at Scopus
  29. Y. Murakami and S. Jones, “SHARP2: protein-protein interaction predictions using patch analysis,” Bioinformatics, vol. 22, no. 14, pp. 1794–1795, 2006. View at Publisher · View at Google Scholar · View at Scopus
  30. S. Jones and J. M. Thornton, “Analysis of protein-protein interaction sites using surface patches,” Journal of Molecular Biology, vol. 272, no. 1, pp. 121–132, 1997. View at Publisher · View at Google Scholar · View at Scopus
  31. A. Via, F. Ferrè, B. Brannetti, and M. Helmer-Citterich, “Protein surface similarities: a survey of methods to describe and compare protein surfaces,” Cellular and Molecular Life Sciences, vol. 57, no. 13-14, pp. 1970–1977, 2000. View at Google Scholar · View at Scopus
  32. W. R. Taylor, A. C. W. May, N. P. Brown, and A. Aszódi, “Protein structure: geometry, topology and classification,” Reports on Progress in Physics, vol. 64, no. 4, pp. 517–590, 2001. View at Publisher · View at Google Scholar · View at Scopus
  33. I. G. Choi, J. Kwon, and S. H. Kim, “Local feature frequency profile: a method to measure structural similarity in proteins,” Proceedings of the National Academy of Sciences of the United States of America, vol. 101, no. 11, pp. 3797–3802, 2004. View at Publisher · View at Google Scholar · View at Scopus
  34. N. Canterakis, “3D zernike moments and zernike affine invariants for 3D image analysis and recognition,” in Proceedings of the 11th Scandinavian Conference on Image Analysis, pp. 85–93, 1999.
  35. R. Mukundan and K. R. Ramakrishnan, “Fast computation of Legendre and Zernike moments,” Pattern Recognition, vol. 28, no. 9, pp. 1433–1442, 1995. View at Publisher · View at Google Scholar · View at Scopus
  36. M. L. Connolly, “Solvent-accessible surfaces of proteins and nucleic acids,” American Association for the Advancement of Science, vol. 221, no. 4612, pp. 709–713, 1983. View at Google Scholar
  37. J. Smith, “Computing a triangulated surface with MSMS. In Vanderbilt University Center for Structural Biology,” 2011, http://structbio.vanderbilt.edu/comp/soft/msms/tutorial.php.
  38. M. Hall, E. Frank, G. Holmes, B. Pfahringer, P. Reutemann, and I. H. Witten, “The WEKA data mining software: an update,” SIGKDD Explorations, vol. 11, no. 1, 2009. View at Google Scholar
  39. R. R. Bouckaert, E. Frank, M. A. Hall et al., “WEKA—experiences with a Java open-source project,” Journal of Machine Learning Research, vol. 11, pp. 2533–2541, 2010. View at Google Scholar · View at Scopus