The Community for Technology Leaders
RSS Icon
Issue No.04 - October-December (2009 vol.6)
pp: 583-593
Yong Wang , Chinese Academy of Sciences, Beijing
Ling-Yun Wu , Chinese Academy of Sciences, Beijing
Ji-Hong Zhang , Beijing Foreign Studies University, Beijing
Zhong-Wei Zhan , China Aerospace Engineering Consultation Center, China
Xiang-Sun Zhang , Chinese Academy of Sciences, Beijing
Luonan Chen , Osaka Sangyo University, Osaka
To unscramble the relationship between protein function and protein structure, it is essential to assess the protein similarity from different aspects. Although many methods have been proposed for protein structure alignment or comparison, alternative similarity measures are still strongly demanded due to the requirement of fast screening and query in large-scale structure databases. In this paper, we first formulate a novel representation of a protein structure, i.e., Feature Sequence of Surface (FSS). Then, a new score scheme is developed to measure the similarity between two representations. To verify the proposed method, numerical experiments are conducted in four different protein data sets. We also classify SARS coronavirus to verify the effectiveness of the new method. Furthermore, preliminary results of fast classification of the whole CATH v2.5.1 database based on the new macrostructure similarity are given as a pilot study. We demonstrate that the proposed approach to measure the similarities between protein structures is simple to implement, computationally efficient, and surprisingly fast. In addition, the method itself provides a new and quantitative tool to view a protein structure.
Protein structure, structure comparison, protein surface.
Yong Wang, Ling-Yun Wu, Ji-Hong Zhang, Zhong-Wei Zhan, Xiang-Sun Zhang, Luonan Chen, "Evaluating Protein Similarity from Coarse Structures", IEEE/ACM Transactions on Computational Biology and Bioinformatics, vol.6, no. 4, pp. 583-593, October-December 2009, doi:10.1109/TCBB.2007.70250
[1] C. Guerra and S. Istrail, Mathematical Methods for Protein Structure Analysis and Design. Springer, 2003.
[2] T. Kawabata and K. Nishikawa, “Protein Structure Comparison Using the Markov Transition Model of Evolution,” Proteins: Structure, Function and Genetics, vol. 41, pp. 108-122, 2000.
[3] I. Eidhammer, I. Jonassen, and W.R. Taylor, “Structure Comparison and Structure Patterns,” J. Computational Biology, vol. 7, no. 7, pp. 685-716, 2000.
[4] L. Holm and C. Sander, “Mapping the Protein Universe,” Science, vol. 273, no. 2, pp. 595-602, Aug. 1996.
[5] O. Carugo and S. Pongor, “Recent Progress in Protein 3D Structure Comparison,” Current Protein and Peptide Science, vol. 3, no. 4, pp. 441-449, Aug. 2002.
[6] L. Chen, T. Zhou, and Y. Tang, “Protein Structure Alignment by Deterministic Annealing,” Bioinformatics, vol. 21, pp. 51-62, 2005.
[7] T. Zhou, L. Chen, Y. Tang, and X.-S. Zhang, “Aligning Multiple Protein Structures by Deterministic Annealing,” J. Bioinformatics and Computational Biology, vol. 3, no. 4, pp. 837-860, 2005.
[8] L. Chen, L.-Y. Wu, R. Wang, Y. Wang, S. Zhang, and X.-S. Zhang, “Comparison of Protein Structures by Multi-Objective Optimization,” Genome Informatics, vol. 16, no. 2, 2005.
[9] L. Chen, L.-Y. Wu, Y. Wang, S. Zhang, and X.-S. Zhang, “Revealing Divergent Evolution, Identifying Circular Permutations and Detecting Active-Sites by Protein Structure Comparison,” BMC Structural Biology, vol. 6, no. 1, p. 18, 2006, 18.
[10] F.E. Cohen and M.J.E. Sternberg, “On the Prediction of Protein Structure: The Significance of the Root-Mean-Square Deviation,” J.Molecular Biology, vol. 138, pp. 321-333, 1980.
[11] O. Carugo, “How Root-Mean-Square Distance (R.M.S.D.) Values Depend on the Resolution of Protein Structures That Are Compared,” J. Applied Crystallography, vol. 36, no. 1, pp. 125-129, Feb. 2003.
[12] O. Carugo and S. Pongor, “A Normalized Root-Mean-Square Distance for Comparing Protein Three-Dimensional Structures,” Protein Science, vol. 10, pp. 1470-1473, 2001.
[13] A. Godzik, “The Structural Alignment between Two Proteins: Is There a Unique Answer?” Protein Science, vol. 5, pp. 1325-1338, 1996.
[14] Y. Wang, L.-Y. Wu, and X.-S. Zhang, “Supervised Classification of Protein Structures Based on Convex Hull Representation,” Int'l J. Bioinformatics Research and Applications, vol. 3, no. 2, 2007.
[15] O. Carugo and S. Pongor, “Protein Fold Similarity Estimated by a Probabilistic Approach Based on C(alpha)-C(alpha) Distance Comparison,” J. Molecular Biology, vol. 315, no. 4, pp. 878-898, Jan. 2002.
[16] K. Vlahovicek, O. Carugo, and S. Pongor, “The PRIDE Server for Protein Three-Dimensional Similarity,” J. Applied Crystallography, vol. 35, pp. 648-649, 2002.
[17] S.D. O'Hearn, A.J. Kusalik, and J.F. Angel, “Molcom: A Method to Compare Protein Molecules Based on 3D Structural and Chemical Similarity,” Protein Eng., vol. 16, no. 3, pp. 169-178, 2003.
[18] A. Caprara, R. Carr, and S. Istrail, “1001 Optimal PDB Structure Alignments: Integer Programming Methods for Finding the Maximum Contact Map Overlap,” J. Computational Biology, vol. 11, no. 1, pp. 27-52, 2004.
[19] P. Rogen and B. Fain, “Automatic Classification of Protein Structure by Using Gauss Integrals,” Proc. Nat'l Academy of Sciences USA (PNAS '03), vol. 100, no. 1, pp. 119-124, Jan. 2003.
[20] P. Rogen and H. Bohr, “A New Family of Global Protein Shape Descriptors,” Math. Biosciences, vol. 182, pp. 167-181, 2003.
[21] N. Krasnogor and D.A. Pelta, “Measuring the Similarity of Protein Structures by Means of the Universal Similarity Metric,” Bioinformatics, vol. 20, no. 7, 2004.
[22] D. Bostick and I.I. Vaisman, “A New Topological Method to Measure Protein Structure Similarity,” Biochemical and Biophysical Research Comm., vol. 304, pp. 320-325, 2003.
[23] T. Kawabata, “MATRAS: A Program for Protein 3D Structure Comparison,” Nucleic Acids Research, vol. 31, no. 13, pp. 3367-3369, 2003.
[24] W. Fang, “The Characterization of a Measure of Information Discrepancy,” Information Sciences, vol. 125, nos. 1-4, pp. 207-232, 2000.
[25] W. Fang, F.S. Roberts, and Z. Ma, “A Measure of Discrepancy of Multiple Sequences,” Information Sciences, vol. 137, pp. 75-102, 2001.
[26] A. Via, F. Ferre, 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, pp. 1970-1977, 2000.
[27] M.L. Connolly, “Molecular Surfaces: A Review,” http://www.netsci. org/Science/Compchemfeature14.html , 1996.
[28] X.-S. Zhang, Z.-W. Zhan, Y. Wang, and L.-Y. Wu, “An Attempt to Explore the Similarity of Two Proteins by Their Surface Shapes,” Operations Research and Its Applications, vol. 5, pp. 276-284, World Publishing Corp., 2005.
[29] J. Leluk, L. Konieczny, and I. Roterman, “Search for Structural Similarity in Proteins,” Bioinformatics, vol. 19, no. 1, pp. 117-124, 2003.
[30] L.P. Chew and K. Kedem, “Finding the Consensus Shape for a Protein Family,” Proc. 18th ACM Symp. Computational Geometry (SoCG), 2002.
[31] A. Caprara and G. Lancia, “Structural Alignment of Large Size Proteins via Lagrangian Relaxation,” Proc. Sixth Ann. Int'l Conf. Computational Biology (RECOMB '02), pp. 100-108, 2002.
[32] H. Yang et al., “The Crystal Structures of Severe Acute Respiratory Syndrome Virus Main Protease and Its Complex with an Inhibitor,” Proc. Nat'l Academy of Sciences USA (PNAS '03), vol. 100, no. 23, pp. 13190-13195, 2003, 100/2313190.
[33] M.A. Marra et al., “The Genome Sequence of the SARS-Associated Coronavirus,” Science, vol. 300, no. 5624, pp. 1399-1404, 2003, .
[34] P.A. Rota et al., “Characterization of a Novel Coronavirus Associated with Severe Acute Respiratory Syndrome,” Science, vol. 300, no. 5624, pp. 1394-1399, 2003, .
[35] K. Anand, J. Ziebuhr, P. Wadhwani, J.R. Mesters, and R. Hilgenfeld, “Coronavirus Main Proteinase (3CLpro) Structure: Basis for Design of Anti-SARS Drugs,” Science, vol. 300, no. 5626, pp. 1763-1767, 2003, .
[36] L. Jin, W. Fang, and H. Tang, “Predicting Protein Structure Class by a New Method of Information Theory,” J. Computational Biology and Chemistry, vol. 27, no. 3, 2003.
[37] J. Liang, H. Edelsbrunner, and C. Woodward, “Anatomy of Protein Pockets and Cavities: Measurement of Binding Site Geometry and Implications for Ligand Design,” Protein Science, vol. 7, pp. 1884-1897, 1998.
[38] T.A. Binkowski, L. Adamian, and J. Liang, “Inferring Functional Relationship of Proteins from Local Sequence and Spatial Surface Patterns,” J. Molecular Biology, vol. 332, pp. 505-526, 2003.
[39] M.B. Swindells, C.A. Orengo, D.T. Jones, E.G. Hutchinson, and J.M. Thornton, “Contemporary Approaches to Protein Structure Classification,” Bioessays, vol. 20, no. 11, pp. 884-891, 1998.
19 ms
(Ver 2.0)

Marketing Automation Platform Marketing Automation Tool