Optimal protein structure alignment using maximum cliques

Operations Research

Volumn 53, Issue 3, 2005, Pages 389-402

  Strickland, Dawn M ^a   Barnes, Earl ^b   Sokol, Joel S ^b  

^a WINTHROP UNIVERSITY   (United States)

^b Georgia Institute of Technology   (United States)

Author keywords

Networks graphs: applications, heuristics; Programming: integer

Indexed keywords

MEDICAL TREATMENTS; NETWORKS/GRAPH: APPLICATIONS; NETWORKS/GRAPH: HEURISTICS; PROTEIN STRUCTURE;

FUNCTIONS; GRAPH THEORY; HEALTH CARE; HEURISTIC METHODS; INTEGER PROGRAMMING; MATHEMATICAL MODELS; OPTIMIZATION; PROBLEM SOLVING; STRUCTURE (COMPOSITION);

PROTEINS;

EID: 25144463996     PISSN: 0030364X     EISSN: 15265463     Source Type: Journal    
DOI: 10.1287/opre.1040.0189     Document Type: Review

References (34)

1. Ahuja, R. K., T. L. Magnanti, J. B. Orlin. 1993. Network Flows. Prentice-Hall, Englewood Cliffs, NJ.
2. Alexandrov, N. N., D. Fischer. 1996. Analysis of topological and non-topological structural similarities in the PDB: New examples from old structures. Protenis 25 354-365.
3. Applegate, D., D. S. Johnson. 1993. dfmax.c [C program]. Available via anonymous ftp from ftp://dimacs.rutgers.edu/pub/challenge/graph/ solvers/.
4. Berman, H. M., J. Westbrook, Z. Feng, G. Gilliland, T. N. Bhat, H. Weissig, I. N. Shindyalov, P. E. Bourne. 2000. The protein data bank. Nucleic Acids Res. 28 235-242.
5. Bomze, I. M., M. Budinich, P. M. Pardalos, M. Pelillo. 1999. The maximum clique problem. D. Z. Du, P. M. Pardalos, eds. Handbook of Combinatorial Optimization, Supplement Vol. A. Kluwer Academic Publishers, Boston, MA, 1-74.
6. Caprara, A., G. Lancia. 2002. Structural alignment of large-size proteins via Lagrangian relaxation. Proc. Sixth Annual Internat. Conf. Computational Biol. ACM Press, New York, 100-108.
7. Caprara, A., R. Can-, S. Istrail, G. Lancia, B. Walenz. 2004. 1001 optimal PDB structure alignments: Integer programming methods for finding the maximum contact map overlap. J. Computational Biol. 11 27-52.
8. Carr, R. D., G. Lancia, S. Istrail. 2000. Branch-and-cut algorithms for independent set problems: Integrality gap and an application to protein structure alignment. Sandia Report SAND2000-2171, Sandia National Laboratories.
9. Carr, R. D., G. Lancia, A. Johnston, S. Istrail, B. Walenz. 2001. Innovative branching strategies with applications to computational biology. Presented at INFORMS International Conference, Maui, Hawaii.
10. Carraghan, R., P. Pardalos. 1990. An exact algorithm for the maximum clique problem. Oper. Res. Lett. 9 375-382.
11. Chen, C.-W. K., D. Y. Y. Yun. 1999. New directions in rough sets, data mining, and granular-soft computing. Lecture Notes Artificial Intelligence 1711 433-442.
12. Dongarra, J. J. 2003. Performance of various computers using standard linear equations software. Computer science technical report CS-89-85, University of Tennessee, Knoxville, TN.
13. Eidhammer, I., I. Jonassen, W. R. Taylor. 2000. Structure comparison and structure patterns. J. Computational Biol. 7 685-716.
14. Gardiner, E., P. Artymiuk, P. Willett. 1997. Clique-detection algorithms for matching three-dimensional molecular structures. J. Molecular Graphics Modeling 15 245-253.
15. Garey, M. R., D. S. Johnson. 1979. Computers and Intractability. W. H. Freeman, San Francisco, CA.
16. Genome International Sequencing Consortium. 2001. Initial sequencing and analysis of the human genome. Nature 409 860-921.
17. Gerstein, M., M. Levitt. 1998. Comprehensive assessment of automatic structural alignment against a manual standard, the SCOP classification of proteins. Protein Sci. 7 445-456.
18. Godzik, A. 1996. The structural alignment between two proteins: Is there a unique answer? Portein Sci. 5 1325-1338.
19. Godzik, A., J. Skolnick, A. Kolinski. 1993. Regularities in interaction patterns of globular proteins. Protein Engrg. 6 801-810.
20. Goldman, D., S. Istrail, C. Papadimitriou. 1999. Algorithmic aspects of protein structure similarity. Proc. 40th Annual IEEE Sympos. Foundations Comput. Sci., IEEE Computer Society, Los Alamitos, CA, 512-522.
21. Holm, L., C. Sander. 1993. Protein structure comparison by alignment of distance matrices. J. Molecular Biol. 233 123-138.
22. Holm, L., C. Sander. 1996. Mapping the protein universe. Science 273 595-602.
23. Jaroszewski, L., W. Li, A. Godzik. 2002. In search for more accurate alignments in the twilight zone. Protein Sci. 11 1702-1713.
24. Jaroszewski, L., L. Rychlewski, A. Godzik. 2000. Improving the quality of twilight-zone alignments. Protein Sci. 9 1487-1496.
25. Kabsch, W. 1978. A discussion of the solution for the best rotation to relate two sets of vectors. Acta Crystallographica A 34 827-828.
26. Kuhn, H. W. 1955. The Hungarian method for the assignment problem. Naval Res. Logist. Quart. 2 83-97.
27. Lancia, G., R. D. Carr, B. Walenz, S. Istrail. 2001. 101 optimal PDB structure alignments: A branch-and-cut algorithm for the maximum contact map overlap problem. Proc. Fifth Annual Internat. Conf. Computational Biol. ACM Press, New York, 193-202.
28. Lesk, A. M. 2001. Introduction to Protein Architecture. Oxford University Press, Oxford, UK.
29. Murzin, A. G., S. E. Brenner, T. Hubbard, C. Chothia. 1995. SCOP: A structural classification of proteins database for the investigation of sequences and structures. J. Molecular Biol. 247 536-540.
30. Orengo, C. A., A. D. Michie, S. Jones, D. T. Jones, M. B. Swindells, J. M. Thornton. 1997. CATH - A hierarchic classification of protein domain structures. Structure 5 1093-1108.
31. Strickland, D. M. 2002. Maximum cliques with application to protein structure alignment. Ph.D. dissertation, School of Industrial and Systems Engineering, Georgia Institute of Technology, Atlanta, GA.
32. Venter, J. C., et al. (paper has over 100 authors). 2001. The sequence of the human genome. Science. 291 1304-1351.
33. Zaki, M. J., S. Jin, C. Bystroff. 2000. Mining residue contacts in proteins. IEEE Internat. Conf. Bioinformatics and Biomedical Engrg. IEEE Computer Society, Los Alamitos, CA, 168-175.
34. Zhao, Y., G. Karypis. 2003. Prediction of contact maps using support vector machines. 3rd IEEE Internat. Sympos. Biolnformatics and Bio-Engineering (BIBE 2003). IEEE Computer Society, Los Alamitos, CA, 26-36.