Fast Protein Structure Alignment

We address the problem of aligning the 3D structures of two proteins. Our pairwise comparisons are based on a new optimization model that is succinctly expressed in terms of linear transformations and highlights the problem's intrinsic geometry. The optimization problem is approximately solved with a new polynomial time algorithm. The worst-case analysis of the algorithm shows that the solution is bounded by a constant depending on the data of the problem.

[1]  Thomas Lengauer,et al.  Proceedings of the Fifth Annual International Conference on Computational Biology, RECOMB 2001, Montréal, Québec, Canada, April 22-25, 2001 , 2001, Annual International Conference on Research in Computational Molecular Biology.

[2]  Robert D. Carr,et al.  1001 Optimal PDB Structure Alignments: Integer Programming Methods for Finding the Maximum Contact Map Overlap , 2004, J. Comput. Biol..

[3]  Timothy F. Havel,et al.  The combinatorial distance geometry method for the calculation of molecular conformation. I. A new approach to an old problem. , 1983, Journal of theoretical biology.

[4]  S. Kearsley.  On the orthogonal transformation used for structural comparisons , 1989 .

[5]  Christos H. Papadimitriou,et al.  Algorithmic aspects of protein structure similarity , 1999, 40th Annual Symposium on Foundations of Computer Science (Cat. No.99CB37039).

[6]  Tim J. P. Hubbard,et al.  Data growth and its impact on the SCOP database: new developments , 2007, Nucleic Acids Res..

[7]  M. Levitt,et al.  Structural similarity of DNA-binding domains of bacteriophage repressors and the globin core , 1993, Current Biology.

[8]  Bartek Wilczynski,et al.  Biopython: freely available Python tools for computational molecular biology and bioinformatics , 2009, Bioinform..

[9]  W. Kabsch,et al.  Dictionary of protein secondary structure: Pattern recognition of hydrogen‐bonded and geometrical features , 1983, Biopolymers.

[10]  Natalio Krasnogor,et al.  Search strategies in structural bioinformatics. , 2008, Current protein & peptide science.

[11]  Wei Xie,et al.  A Reduction-Based Exact Algorithm for the Contact Map Overlap Problem , 2007, J. Comput. Biol..

[12]  F. Makedon,et al.  A bipartite graph matching framework for finding correspondences between structural elements in two proteins , 2004, The 26th Annual International Conference of the IEEE Engineering in Medicine and Biology Society.

[13]  T. N. Bhat,et al.  The Protein Data Bank , 2000, Nucleic Acids Res..

[14]  A. Godzik.  The structural alignment between two proteins: Is there a unique answer? , 1996, Protein science : a publication of the Protein Society.

[15]  Harvey J. Greenberg,et al.  Quadratic Binary Programming Models in Computational Biology , 2008, Algorithmic Oper. Res..

[16]  Rita Casadio,et al.  Algorithms in Bioinformatics, 5th International Workshop, WABI 2005, Mallorca, Spain, October 3-6, 2005, Proceedings , 2005, WABI.

[17]  Nabil H. Mustafa,et al.  Fast Molecular Shape Matching Using Contact Maps , 2007, J. Comput. Biol..

[18]  Lenore Cowen,et al.  Matt: Local Flexibility Aids Protein Multiple Structure Alignment , 2008, PLoS Comput. Biol..

[19]  Robert D. Carr,et al.  101 optimal PDB structure alignments: a branch-and-cut algorithm for the maximum contact map overlap problem , 2001, RECOMB.

[20]  Rachel Kolodny,et al.  Comprehensive evaluation of protein structure alignment methods: scoring by geometric measures. , 2005, Journal of molecular biology.

[21]  Joel Sokol,et al.  Optimal Protein Structure Alignment Using Maximum Cliques , 2005, Oper. Res..

[22]  W. Kabsch.  A discussion of the solution for the best rotation to relate two sets of vectors , 1978 .

[23]  Nathan Linial,et al.  Approximate protein structural alignment in polynomial time. , 2004, Proceedings of the National Academy of Sciences of the United States of America.

[24]  Rumen Andonov,et al.  An Efficient Lagrangian Relaxation for the Contact Map Overlap Problem , 2008, WABI.

[25]  J. Augsburger,et al.  A new approach to an old problem. , 1999, Survey of ophthalmology.