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Issue No.06 - November/December (2011 vol.8)
pp: 1716-1720
Aleksandar Poleksic , University of Northern Iowa, Cedar Falls
Protein structure alignment is an important tool in many biological applications, such as protein evolution studies, protein structure modeling, and structure-based, computer-aided drug design. Protein structure alignment is also one of the most challenging problems in computational molecular biology, due to an infinite number of possible spatial orientations of any two protein structures. We study one of the most commonly used measures of pairwise protein structure similarity, defined as the number of pairs of atoms in two proteins that can be superimposed under a predefined distance cutoff. We prove that the expected running time of a recently published algorithm for optimizing this (and some other, derived measures of protein structure similarity) is polynomial.
Protein structure, structural alignment.
Aleksandar Poleksic, "Optimizing a Widely Used Protein Structure Alignment Measure in Expected Polynomial Time", IEEE/ACM Transactions on Computational Biology and Bioinformatics, vol.8, no. 6, pp. 1716-1720, November/December 2011, doi:10.1109/TCBB.2011.122
[1] M.G. Rossmann and P. Argos, “The Taxonomy of Binding sites in Proteins,” Moleculer and Cellular Biochemistry, vol. 21, pp. 161-182, 1978.
[2] J. Moult, K. Fidelis, A. Kryshtafovych, B. Rost, and A. Tramontano, “Critical Assessment of Methods of Protein Structure Prediction—Round VIII,” Proteins, vol. 77, no. (S9), pp. 1-4, 2009.
[3] D. Fischer, L. Rychlewski, R.L. Dunbrack, A.R. Ortiz, and A. Elofsson, “CAFASP3: The Third Critical Assessment of Fully Automated Structure Prediction Methods,” Proteins, vol. 53, no. (S6), pp. 503-516, 2003.
[4] I.Y. Koh et al. “EVA: Evaluation of Protein Structure Prediction Servers,” Nucleic Acids Research, vol. 31, pp. 3311-3315, 2003.
[5] L. Rychlewski and D. Fischer, “LiveBench-8: The Large-Scale, Continuous Assessment of Automated Protein Structure Prediction,” Protein Science, vol. 14, pp. 240-245, 2005.
[6] X. Pennec and N. Ayache, “An $O(n^{2})$ Algorithm for 3D Substructure Matching of Proteins: Shape and Pattern Matching in Computational Biology,” Proc. First Int'l Workshop Shape and Pattern Matching in Computational Biology, pp. 25-40, 1994.
[7] X. Pennec and N. Ayache, “A Geometric Algorithm to Find Small but Highly Similar 3D Substructures in Proteins,” Bioinformatics, vol. 14, pp. 516-522, 1998.
[8] N.S. Boutonnet, M.J. Rooman, M.E. Ochagavia, J. Richelle, and S.J. Wodak, “Optimal Protein Structure Alignments by Multiple Linkage Clustering: Application to Distantly Related Proteins,” Protein Eng., vol. 8, pp. 647-662, 1995.
[9] S. Goldsmith-Fischman and B. Honig, “Structural Genomics: Computational Methods for Structure Analysis,” Protein Science, vol 12, pp. 1813-1821, 2003.
[10] H. Hasegawa and L. Holm, “Advances and Pitfalls of Protein Structural Alignment,” Current Opinion Structural Biology, vol. 19, pp. 341-348, 2009.
[11] O. Carugo, “Recent Progress in Measuring Structural Similarity between Proteins,” Current Protein and Peptide Science, vol. 8, pp. 219-241, 2007.
[12] O. Carugo and S. Pongor, “Recent Progress in Protein 3D Structure Comparison,” Current Protein and Peptide Science, vol. 3, pp. 441-449, 2002.
[13] D. Goldman, C.H. Papadimitriou, and S. Istrail, “Algorithmic Aspects of Protein Structure Similarity,” Proc. 40th Ann. Symp. Foundations of Computer Science, pp. 512-522, 1999.
[14] A. Caprara, R. Carr, S. Istrail, G. Lancia, and B. Walenz, “1001 Optimal PDB Structure Alignments, Integer Programming Methods for Finding the Maximum Contact Map Overlap,” J. Computational Biology, vol. 11, pp. 27-52, 2004.
[15] Y. Zhang and J. Skolnick, “TM-Align: A Protein Structure Alignment Algorithm Based on the TM-Score,” Nucleic Acids Research, vol. 33, pp. 2302-2309, 2005.
[16] I. Eidhammer, I. Jonassen, and W.R. Taylor, “Structure Comparison and Structure Patterns,” J. Computational Biology, vol. 7, pp. 685-716, 2000.
[17] M. Gerstein and M. Levitt, “Using Iterative Dynamic Programming to Obtain Accurate Pairwise and Multiple Alignments of Protein Structures,” Proc. Fourth Int'l Conf. Intelligent Systems for Molecular Biology, pp. 59-67, 1996.
[18] M. Levitt M and M. Gerstein, “A Unified Statistical Framework for Sequence Comparison and Structure Comparison,” Proc. Nat'l Academy of Sciences USA, vol. 95, pp. 5913-5920, 1998.
[19] A.P. Singh and D.L. Brutlag, “Hierarchical Protein Structure Superposition Using Both Secondary Structure and Atomic Representations,” Proc. Int'l Conf. Intelligent Systems for Molecular Biology, vol. 5, pp. 284-293, 1997.
[20] S.B. Pandit and J. Skolnick, “Fr-TM-Align: A New Protein Structural Alignment Method Based on Fragment Alignments and the TM-Score,” BMC Bioinformatics, vol. 9, article no. 531, 2008.
[21] Z.K. Feng and M.J. Sippl, “Optimum Superposition of Protein Structures: Ambiguities and Implications,” Folding and Design, vol. 1, pp. 123-132, 1996.
[22] J. Xu, F. Jiao, and B. Berger, “A Parameterized Algorithm for Protein Structure Alignment,” J. Computational Biology, vol. 14, pp. 564-577, 2007.
[23] R. Kolodny and N. Linial, “Approximate Protein Structural Alignment in Polynomial Time,” Proc. Nat'l Academy of Sciences USA, vol. 101, pp. 12201-12206, 2003.
[24] A. Poleksic, “Algorithms for Optimal Protein Structure Alignment,” Bioinformatics, vol. 25, pp. 2751-2756, 2009.
[25] C. Ambühl, S. Chakraborty, and B. Gärtner, “Computing Largest Common Point Sets under Approximate Congruence,” Proc. Eighth Ann. European Symp. Algorithms, pp. 52-64, 2000.
[26] S.C. Li, D. Bu, J. Xu, and M. Li, “Finding Largest Well-Predicted Subset of Protein Structure Models,” Proc. Combinatorial Pattern Matching, pp. 44-55, 2008.
[27] A. Zemla, “LGA—A Method for Finding 3D Similarities in Protein Structures,” Nucleic Acids Research, vol. 31, pp. 3370-3374, 2003.
[28] N. Siew, A. Elofsson, L. Rychlewski, and D. Fischer, “MaxSub: An Automated Measure for the Assessment of Protein Structure Prediction Quality,” Bioinformatics, vol. 16, pp. 776-785, 2000.
[29] A. Sali and T.L. Blundell, “Comparative Protein Modeling by Satisfaction of Spatial Restraints,” J. Molecular Biology, vol. 234, pp. 779-815, 1993.
[30] T.F. Smith and M.S. Waterman, “Identification of Common Molecular Subsequences,” J. Molecular Biology, vol. 147, pp. 195-197, 1981.
[31] A. Poleksic, “Optimal Protein Structure Alignment in Sub-Quadratic Time,” Proc. Fifth Int'l ICST Conf. Bio-Inspired Models of Network (BIONETICS '10), 2010.
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