A parameterized algorithm for protein structure alignment

Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)

Volumn 3909 LNBI, Issue , 2006, Pages 488-499

  Xu, Jinbo ^a,b   Jiao, Feng ^c   Berger, Bonnie ^a  

^a MASSACHUSETTS INSTITUTE OF TECHNOLOGY   (United States)

^b TOYOTA TECHNOLOGICAL INSTITUTE AT CHICAGO   (United States)

^c UNIVERSITY OF WATERLOO   (Canada)

Author keywords

[No Author keywords available]

Indexed keywords

ALIGNMENT; COMPUTER OPERATING SYSTEMS; DECOMPOSITION; GENETIC ALGORITHMS; MOLECULAR STRUCTURE; PARAMETER ESTIMATION; POLYNOMIAL APPROXIMATION;

LINUX; POLYNOMIAL-TIME APPROXIMATION; PROTEIN STRUCTURE ALIGNMENT; RIGID-BODY TRANSFORMATION;

PROTEINS;

EID: 33745766839     PISSN: 03029743     EISSN: 16113349     Source Type: Book Series    
DOI: 10.1007/11732990_41     Document Type: Conference Paper

References (25)

1. M. Comin, C.Guerra, and G. Zanotti. PROuST: a comparison method of three-dimensional structures of proteins using indexing techniques. Journal of Computational Biology, 11(6):1061-1072, 2004.
2. L. Holm and C. Sander. Protein structure comparison by alignment of distance matrices. Journal of Molecular Biology, 233:123-138, 1993.
3. N.N. Alexandrav. SARFing the PDB. Protein Engineering, 9:727-732, 1996.
4. M. Gerstein and M. Levitt. Using iterative dynamic programming to obtain accurate pairwise and multiple alignments of protein structures. In Proceedings of International Conference on Intelligent Systems in Molecular Biology, pages 59-67, 1996.
5. A.P. Singh and D.L. Brutlag. Hierarchical protein structure superposition using both secondary structure and atomic representations. In Proceedings of International Conference on Intelligent Systems in Molecular Biology, pages 284-93, 1997.
6. J.F. Gibrat, T. Madej, and S.H. Bryant. Surprising similarities in structure comparison. Current Opinion in Structural Biology, (6):377-385, 1996.
7. T. Akutsu and H. Tashimo. Protein structure comparison using representation by line segment sequences. In Proceedings of Pacific Symposium on Biocomputing '96 (PSB'96), pages 25-40, 1996.
8. G. Lancia, R. Carr, B. Walenz, and S. Istrail. 101 optimal PDB structure alignments: a branch-and-cut algorithm for the maximum contact map overlap problem. In RECOMB 2001, pages 193-202. ACM Press, 2001.
9. A. Caprara and G. Lancia. Structural alignment of largesize proteins via Lagrangian relaxation. In RECOMB 2002, pages 100-108. ACM Press, 2002.
10. G. Lancia and S. Istrail. Protein structure comparison: Algorithms and applications. In Mathematical Methods for Protein Structure Analysis and Design, volume 2666 of Lecture Notes in Computer Science, pages 1-33, 2003.
11. C. Lemmen and T. Lengauer. Computational methods for the structural alignment of molecules. Journal of Computer-Aided Molecular Design, 14:215-232, 2000.
12. R. Kolodny and N. Linial. Approximate protein structural alignment in polynomial time. PNAS, 101(33):12201-12206, 2004.
13. D. Goldman, C.H. Papadimitriou, and S. Istrail. Algorithmic aspects of protein structure similarity. In FOCS 99: Proceedings of the 40th Annual Symposium on Foundations of Computer Science, pages 512-522. IEEE Computer Society, 1999.
14. I.N. Shindyalov and P.E. Bourne. Protein structure alignment by incremental combinatorial extension (CE) of the optimal path. Protein Engineering, 11(9):739-747, 1998.
15. O. Verbitsky. On the largest common subgraph problem, 1994. Unpublished manuscript.
16. S. Jokisch and H. Müller. Inter-point-distance-dependent approximate point set matching. Technical Report Research Report No. 653, 1997.
17. X. Yuan and C. Bystroff. Non-sequential structure-based alignments reveal topology-independent core packing arrangements in proteins. Bioinformatics, 27:1010-1019, 2005.
18. O. Dror, H. Benyamini, R. Nussinov, and H. Wolfson. MASS: Multiple structural alignment by secondary structures. Bioinformatics, 19(Suppl. 1):95-104, 2003.
19. J. Zhu and Z. Weng. FAST: A novel protein structure alignment algorithm. Proteins: Structure Function, and Bioinformatics, 2004. In Press.
20. H.M. Berman, J. Westbrook, Z. Feng, G. Gilliland, T.N. Bhat, H. Weissig, I.N. Shindyalov, and P.E. Bourne. The protein data bank. Nucleic Acids Research, 28:235-242, 2000.
21. K.S. Arun, T.S. Huang, and S.D. Blostein. Least-square fitting of two 3-d point sets. IEEE Trans. on Pattern Analysis and Machine Intelligence, 9(5):698-700, 1987.
22. N. Robertson and P.D. Seymour. Graph minors. II. algorithmic aspects of tree-width. Journal of Algorithms, 7:309-322, 1986.
23. J. Xu. Rapid side-chain packing via tree decomposition. In RECOMB 2005, volume 3500 of Lecture Notes in Bioinformatics. Springer, May 2005.
24. M.H. Hao, S. Rackovsky, A. Liwo, M.R. Pincus, and H.A. Scheraga. Proc. Natl. Acad. Sci. USA, 89:6614-6618, 1992.
25. A. Caprara, R. Carr, S. Istrail, G. Lancia, and B. Walenz. 101 optimal PDB structure alignments: a branch-and-cut algorithm for the maximum contact map overlap problem. Journal of Computational Biology, 11(1):27-52, 2004.