The URMS-RMS hybrid algorithm for fast and sensitive local protein structure alignment

Journal of Computational Biology

Volumn 12, Issue 1, 2005, Pages 12-32

  Yona, Golan ^a   Kedem, Klara ^a,b  

^a Department of Computer Science and School of Operations Research and Information Engineering   (United States)

^b BEN GURION UNIVERSITY OF THE NEGEV   (Israel)

Author keywords

Protein structure comparison; SCOP

Indexed keywords

ALGORITHM; ARTICLE; CLASSIFICATION; CLUSTER ANALYSIS; COMPUTER PROGRAM; DYNAMICS; HYBRID ALGORITHM; PRIORITY JOURNAL; PROTEIN DOMAIN; PROTEIN STRUCTURE; ROOT MEAN SQUARED METRIC ALGORITHM; ROTATION; SCOP CLASSIFICATION; SCORING SYSTEM; STATISTICAL MODEL; STATISTICAL SIGNIFICANCE; STRUCTURE ANALYSIS; UNIT VECTOR ROOT MEAN SQUARED METRIC HYBRID ALGORITHM;

ALGORITHMS; COMPUTATIONAL BIOLOGY; DATABASES, PROTEIN; PROTEIN STRUCTURE, TERTIARY; PROTEINS; SOFTWARE; STRUCTURAL HOMOLOGY, PROTEIN;

EID: 13444259496     PISSN: 10665277     EISSN: None     Source Type: Journal    
DOI: 10.1089/cmb.2005.12.12     Document Type: Article

References (29)

1. Brenner, S.E., Koehl, P., and Levitt, M. 2000. The astral compendium for protein structure and sequence analysis. Nucl. Acids Res. 28, 255-256.
2. Chew, L.P., Kedem, K., Huttenlocher, D.P., and Kleinberg, J. 1999. Fast detection of geometric substructure in proteins. J. Comp. Biol. 6(3-4), 313-325.
3. Chew, L.P., and Kedem, K. 2002. Finding the consensus shape for a protein family. Proc. ACM 18th Symp. on Computational Geometry, 64-73.
4. Dayhoff, M.O., Schwartz, R.M., and Orcutt, B.C. 1978. A model of evolutionary change in proteins, in M. Dayhoff, ed., Atlas of Protein Sequence and Structure, vol. 5, suppl. 3, 345-352, National Biomedical Research Foundation, Silver Spring, MD.
5. Dembo, A., Karlin, S., and Zeitouni, O. 1994. Critical phenomena for sequence matching with scoring. Ann. Prob. 22, 1993-2021.
6. Fischer, D., Nussinov, R., and Wolfson, H. 1992. 3D substructure matching in protein molecules. Proc. 3rd Intl. Symp. Combinatorial Pattern Matching, 136-150.
7. Gerstein, M., and Levitt, M. 1996. Using iterative dynamic programming to obtain accurate pairwise and multiple alignments of protein structures. Proc. of ISMB'96 Intelligent Systems for Molecular Biology, 59-66.
8. Gerstein, M., and Levitt, M. 1998. Comprehensive assessment of automatic structural alignment against a manual standard, the SCOP classification of proteins. Protein Sci. 7, 445-456.
9. Griendley, H.M., Artymiuk, P.J., Rice, D.W., and Willett, P. 1993. Identification of tertiary structure resemblance in proteins using a maximal comrion subgraph isomorphism algorithm. J. Mol. Biol. 229, 707-721.
10. Gumbel, E.J. 1958. Statistics of Extremes, Columbia University Press, New York.
11. Holm, L., and Sander, C. 1993. Protein structure comparison by alignment of distance matrices. J. Mol. Biol. 233, 123-138.
12. Holm, L., and Sander, C. 1996. Mapping the protein universe. Science 273, 595-602.
13. Hubbard, T.J., Ailey, B., Brenner, S.E., Murzin, A.G., and Chothia, C. 1999. SCOP: A structural classification of proteins database. Nucl. Acids Res. 27, 254-256.
14. Karlin, S., and Altschul, S.F. 1990. Methods for assessing the statistical significance of molecular sequence features by using general scoring schemes. Proc. Natl Acad. Sci. USA 87, 2264-2268.
15. Kedem, K., Chew, L.P., and Elber, R. 1999. Unit-vector RMS (URMS) as a tool to analyze molecular dynamics trajectories. Proteins Struct. Funct. Genet. 37, 554-564.
16. Levitt, M., and Gerstein, M. 1998. A unified statistical framework for sequence comparison and structure comparison. Proc. Natl. Acad. Sci. USA 95, 5913-5920.
17. Orengo, C.A., Brown, N.P., and Taylor, W.R. 1992. Fast structure alignment for protein databank searching. Proteins Struct. Funct. Genet. 14, 139-167.
18. Ortiz, A.R., Strauss, C.E.M., and Olmeda, O. 2002. MAMMOTH (Matching molecular models obtained from theory): An automated method for model comparison. Protein Sci. 11, 2606-2621.
19. Pennec, X., and Ayache, N. 1998. A geometric algorithm to find small but highly similar 3D substructures in proteins. Bioinformatics 14, 516-522.
20. Rackovsky, S., and Scheraga, H.A. 1978. Differential geometry and polymer conformations 2. Development of a conformational distance function. Macromolecules 13, 1440-1453.
21. Rackovsky, S., and Goldstein, D.A. 1998. Protein comparison and classification: A differential geometry approach. Proc. Nat. Acad. Sci. 85, 777-781.
22. 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.
23. Siew, N., Elofsson, A., Rychlewski, L., and Fischer, D. 2000. MaxSub: An automated measure for the assessment of protein structure prediction quality. Bioinformatics 16, 776-785.
24. Taylor, W.R. 1999. Protein stucture alignment using iterated double dynamic programming. Protein Sci. 8, 654-665.
25. Taylor, W.R., and Orengo, C.A. 1989. Protein structure alignment. J. Mol. Biol. 208, 1-22.
26. Vriend, G., and Sander, C. 1991. Detection of common three-dimensional substructures in proteins. Proteins Struct. Funct. Genet. 11, 52-58.
27. Yee, D., and Dill, K. 1993. Families and the structural relatedness among globular proteins. Protein Sci. 2, 884-899.
28. Yona, G., and Levitt, M. 2000. Towards a complete map of the protein space based on a unified sequence and structure analysis of all known proteins. Proc. of ISMB 2000, 395-406.
29. Yona, G., Linial, N., and Linial, M. 1999. ProtoMap: Automatic classification of protein sequences, a hierarchy of protein families, and local maps of the protein space. Proteins 37, 360-378.