Fast overlapping of protein contact maps by alignment of eigenvectors

Bioinformatics

Volumn 26, Issue 18, 2010, Pages 2250-2258

  di Lena, Pietro ^a   Fariselli, Piero ^a   Margara, Luciano ^a   Vassura, Marco ^a   Casadio, Rita ^a  

^a UNIVERSITY OF BOLOGNA   (Italy)

Author keywords

[No Author keywords available]

Indexed keywords

PROTEIN;

ALGORITHM; ARTICLE; BIOLOGY; CHEMISTRY; COMPARATIVE STUDY; METHODOLOGY; PHYSIOLOGY; PROTEIN CONFORMATION; VALIDATION STUDY;

ALGORITHMS; COMPUTATIONAL BIOLOGY; PROTEIN CONFORMATION; PROTEINS;

EID: 77956526859     PISSN: 13674803     EISSN: 14602059     Source Type: Journal    
DOI: 10.1093/bioinformatics/btq402     Document Type: Article

References (40)

1. Agarwal,P.K. et al. (2007) Fast molecular shape matching using contact maps. J. Comput. Biol., 14, 131-143.
2. Altschul,S.F. et al. (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res., 25, 3389-3402.
3. Andonov,R. et al. (2008) An efficient Lagrangian relaxation for the contact map overlap problem. Lect. Notes Bioinform., 5251, 162-173. Supplementary material available at http://www.irisa.fr/symbiose/old/softwares/resources/proteus300
4. Andreeva,A. et al. (2008) Data growth and its impact on the SCOP database: new developments. Nucleic Acids Res., 36, 419-425.
5. Andrews,H.C. and Patterson,C.L. (1976) Singular value decomposition (SVD) image coding. IEEE Trans. Commun., 24, 425-432.
6. Bartoli,L. et al. (2007) The effect of backbone on the small-world properties of protein contact maps. Phys. Biol., 4, 1-5.
7. Caprara,A. and Lancia,G. (2002) Structural alignment of large-size proteins via Lagrangian relaxation. In Proceedings of the Annual International Conference on Computational Molecular Biology (RECOMB 2002), Washington, DC, USA, pp. 100-108.
8. Caprara,A. et al. (2004) 1001 optimal PDB structure alignments: integer programming methods for finding the maximum contact map overlap. J. Comput. Biol., 11, 27-52.
9. Duarte,J.M. et al. (2010) Optimal contact definition for reconstruction of contact maps. BMC Bioinformatics, 11, 283.
10. Ezkurdia,I. et al. (2009) Assessment of domain boundary predictions and the prediction of intramolecular contacts in CASP8. Proteins, 77, 96-209.
11. Fischer,D. et al. (1996) Assessing the performance of fold recognition methods by means of a comprehensive benchmark. In Proceedings of the Pacific Symposium on Biocomputing 1996, The Big Island of Hawaii, USA, pp. 300-318.
12. Godzik,A. (1996) The structural alignment between two proteins: is there a unique answer? Protein Sci., 5, 1325-1338.
13. Godzik,A. et al. (1992) Topology fingerprint approach to the inverse protein folding problem. J. Mol. Biol., 227, 227-238.
14. Goldman,D. et al. (1999) Algorithmic aspects of protein structure similarity. In Proceedings of the 40th Annual Symposium on Foundations of Computer Science, New York City, NY, USA, pp. 512-521.
15. Holm,L. and Sander,C. (1993) Protein structure comparison by alignment of distance matrices. J. Mol. Biol., 233, 123-138.
16. Holm,L. and Park,J. (2000) DaliLite workbench for protein structure comparison. Bioinformatics, 16, 566-567.
17. Jain,B.J. and Lappe,M. (2007) Joining softassign and dynamic programming for the contact map overlap problem. Lect. Notes Bioinform., 4414, 410-423.
18. Jain,B.J. and Obermayer,K (2009) BIMAL: Bipartite matching alignment for the contact map overlap problem. In Proceedings of the International Joint Conference on Neural Networks, Atlanta, Georgia, USA, pp. 1394-1400.
19. Kabsch,W. (1976) A solution for the best rotation to relate two sets of vectors. Acta Cryst., 32, 922-923.
20. Krasnogor,N. and Pelta, D.A. (2004) Measuring the similarity of protein structures by means of the universal similarity metric. Bioinformatics, 20, 1015-1021.
21. Lancia,G. et al. (2001) 101 Optimal PDB structure alignments: a branch-and-cut algorithm for the maximum contact map overlap problem. In Proceedings of the Annual International Conference on Computational Molecular Biology, RECOMB 2001, Montreal, Quebéc, Canada, pp. 193-202.
22. Luo,B. and Hancock,E. (2001) Structural graph matching using the EM algorithm and singular value decomposition. IEEE Trans. Pattern Anal. Mach. Intell., 23, 1120-1136.
23. Needleman,S.B. and Wunsch,C.D. (1970)Ageneral method applicable to the search for similarities in the amino acid sequence of two proteins. J. Mol. Biol., 48, 443-453.
24. Oakley,M.T. et al. (2008) Search strategies in structural bioinformatics. Curr. Protein Pept. Sci., 9, 260-274.
25. Pelta,D.A. et al. (2008) A simple and fast heuristic for protein structure comparison. BMC Bioinformatics, 9, 161.
26. Porto,M. et al. (2004) Reconstruction of protein structures from a vectorial representation. Phys. Rev. Lett., 92, 218101.
27. Rahmati,S. and Glasgow,J.I. (2009) Comparing protein contact maps via Universal Similarity Metric: an improvement in the noise-tolerance. Int. J. Comput. Biol. Drug Des., 2, 149-167.
28. Robles-Kelly,A. and Hancock A.R. (2002) String edit distance, random walks and graph matching. Lect. Notes Comput. Sci., 2396, 104-112.
29. Sadreyev,R.I. et al. (2009) Discrete-continuous duality of protein structure space. Curr. Opin. Struct. Biol., 19, 321-328.
30. Shindyalov,I.N. and Bourne,P.E. (1998) Protein structure alignment by incremental combinatorial extension (CE) of the optimal path. Protein Eng., 11, 739-747.
31. Singh,R. et al. (2007) Pairwise global alignment of protein interaction networks by matching neighborhood topology. Lect. Notes Comput. Sci., 4453, 16-31.
32. Strang,G. (2003) Introduction to Linear Algebra.Wellesley-Cambridge Press,Wellesley, MA.
33. Strickland,D.M. et al. (2005) Optimal protein structure alignment using maximum cliques. Oper. Res., 53, 389-402.
34. Umeyama,S. (1988) Eigendecomposition approach to weighted graph matching problems. IEEE Trans. Pattern Anal. Mach. Intell., 10, 695-703.
35. Vassura,M. et al. (2008) Reconstruction of 3D structures from protein contact maps. IEEE/ACM Trans. Comput. Biol. Bioinform., 5, 357-366.
36. Vassura,M. et al. (2008) FT-COMAR: fault tolerant three-dimensional structure reconstruction from protein contact maps. Bioinformatics, 24, 1313-1315.
37. Xie,W. and Sahinidis,N.V. (2007) A reduction-based exact algorithm for the contact map overlap problem. J. Comput. Biol., 14, 637-654.
38. Xu,J. et al. (2007)Aparameterized algorithm for protein structure alignment. J. Comput. Biol., 14, 564-577.
39. Zhang,Y. and Skolnick,J. (2005) TM-align: a protein structure alignment algorithm based on the TM-score. Nucleic Acids Res., 22, 2302-2309.
40. Zhao,G. et al. (2007) Using eigen-decomposition method for weighted graph matching. Lect. Notes Comput. Sci., 4453, 1283-1294.