A fuzzy sets based generalization of contact maps for the overlap of protein structures

Fuzzy Sets and Systems

Volumn 152, Issue 1, 2005, Pages 103-123

  Pelta, David ^a   Krasnogor, Natalio ^b   Bousono Calzon, Carlos ^c   Verdegay, José L ^a   Hirst, J ^d   Burke, Edmund ^b  

^a UNIVERSITY OF GRANADA   (Spain)

^b Optimisation Plan Res Grp U   (United Kingdom)

^c UNIVERSIDAD CARLOS III DE MADRID   (Spain)

^d UNIVERSITY OF NOTTINGHAM   (United Kingdom)

Author keywords

FANS; Fuzzy sets; Maximum contact map overlap; Protein structure alignment; Protein structure comparison; Universal similarity metric

Indexed keywords

ALGORITHMS; BIOTECHNOLOGY; COMPUTATIONAL METHODS; MEMBERSHIP FUNCTIONS; MOLECULAR STRUCTURE; NUCLEAR MAGNETIC RESONANCE; PROTEINS; X RAY CRYSTALLOGRAPHY;

FUZZY ADAPTIVE NEIGHBOURHOOD SEARCH (FANS); MAXIMUM CONTACT MAP OVERLAP; PROTEIN STRUCTURE ALIGNMENT; PROTEIN STRUCTURE COMPARISON; UNIVERSAL SIMILARITY METRIC;

FUZZY SETS;

EID: 15344350283     PISSN: 01650114     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.fss.2004.10.017     Document Type: Article

References (28)

1. P. Artimiuk, A. Poirrette, D. Rice, and P. Willett The use of graph theoretical methods for the comparison of the structure of biological macromolecules Topics of Current Chem. 174 1995 73 103
2. H. Berman, J. Westbrook, Z. Feng, G. Gilliland, T. Bhat, H. Weissing, I. Shindyalov, and P. Bourne The protein data bank Nucleic Acids Res. 28 2000 235 242
3. A. Blanco, D. Pelta, and J. Verdegay A fuzzy valuation-based local search framework for combinatorial problems J. Fuzzy Optim. Decision Making 1 2 2002 177 193
4. P. Bourne, and I. Shindyallov Structure comparison and alignment Structural Bioinformatics 2003 Wiley-Liss New York
5. 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. Comput. Biol. 11 1 2004 27 52
6. A. Caprara, and G. Lancia Structural alignment of large-size proteins via lagrangian relaxation Proc. RECOMB 2002 2002 ACM New York
7. B. Carr, W. Hart, N. Krasnogor, E. Burke, J. Hirst, and J. Smith Alignment of protein structures with a memetic evolutionary algorithm GECCO-2002: Proc. Genetic and Evolutionary Comput. Conf. Morgan Kaufman, Los Altos, CA 2002
8. H. Chan, and K. Dill Origins of structure in globular proteins Proc. Nat. Acad. Sci. USA 97 1990 6388 6392
9. L. Chew, and K. Kedem Finding consensus shape for a protein family 18th ACM Symp. on Computational Geometry 2002 Barcelona Spain
10. D. Goldman, Ph.D. Thesis, Department of Computer Sciences, UC Berkeley, 2000.
11. D. Goldman, S. Istrail, C. Papadimitriou, Algorithmic aspects of protein structure similarity, in: Proc. 40th Annu. IEEE Symp. on Foundations of Computer Science, 1999, pp. 512-522.
12. P. Hansen, N. Mladenovic, Variable neighborhood search: principles and applications, European J. Oper. Res. (130) (2001) 449-467.
13. L. Holm, C. Sander, Protein structure comparison by alignment of distance matrices, J. Molecular Biol. (1993) 123-138.
14. L. Holm, and C. Sander Mapping the protein universe Science 273 1996 595 602
15. P. Koehl Protein structure similarities Current Opinion Struct. Biol. 11 2001 348 353
16. N. Krasnogor, Studies on the theory and design space of memetic algorithms, Ph.D. Thesis, Faculty of Computing, Mathematics and Engineering, University of the West of England, Bristol, UK, 2002.
17. N. Krasnogor Self-generating metaheuristics in bioinformatics the proteins structure comparison case Genetic Programming Evolvable Mach. 5 2 2004
18. N. Krasnogor, D.A. Pelta, Multimeme algorithms using fuzzy logic based memes, In: W. Hart, N. Krasnogor, J. Smith (Eds.), Recent Advances in Memetic Algorithms and Related Search Technologies, Studies in Fuzziness and Soft Computing, Springer, Berlin, 2004, pp. 49-64.
19. N. Krasnogor, D. Pelta, Fuzzy memes in multimeme algorithms: a fuzzy-evolutionary hybrid, Fuzzy Sets based Heuristics for Optimization, Studies in Fuzziness and Soft Computing, Physica-Verlag, Wurzburg, 2003, pp. 1-20.
20. N. Krasnogor, D. Pelta, Measuring the similarity of protein structures by means of the universal similarity metric, Bioinformatics (7) (2004) 1015-1021.
21. G. Lancia, R. Carr, B. Walenz, S. Istrail, 101 optimal pdb structure alignments: a branch-and-cut algorithm for the maximum contact map overlap problem, Proc. Fifth Annu. Internat. Conf. on Computational Molecular Biology, RBCOMB 2001, 2001.
22. R.A. Laskowski Structural quality assurance Structural Bioinformatics 2003 Wiley-Liss New York
23. J. Leluk, L. Konieczny, and I. Roterman Search for structural similarity in proteins Bioinformatics 19 1 2003 117 124
24. S. Lifson, and C. Sander Antiparallel and parallel beta-strands differ in amino acid residue preferences Nature 282 1979 109 111
25. L. Mirny, and E. Domany Protein fold recognition and dynamics in the space of contact maps Proteins 26 1996 391 410
26. D. Pelta, A. Blanco, J.L. Verdegay, Fuzzy adaptive neighborhood search: examples of application, Fuzzy Sets Based Heuristics for Optimization, Studies in Fuzziness and Soft Computing, Physica-Verlag, Wurzburg, 2003, to appear.
27. W. Taylor Protein structure comparison using iterated double dynamic programming Protein Sci. 8 1999 654 665
28. T. Wu, S. Schmidler, T. Hastie, and D. Brutlag Regression analysis of multiple protein structures J. Comput. Biol. 5 1998 585 595