Fast detection of common geometric substructure in proteins

Journal of Computational Biology

Volumn 6, Issue 3-4, 1999, Pages 313-325

  Chew, L Paul ^a   Huttenlocher, Dan ^a   Kedem, Klara ^b   Kleinberg, Jon ^a  

^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

Efficient algorithms; Structure matching; Unit vector RMS

Indexed keywords

CONFERENCE PAPER; CONFORMATIONAL TRANSITION; GEOMETRY; MATHEMATICAL MODEL; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN DOMAIN; PROTEIN STRUCTURE;

ALGORITHMS; BIOMETRY; DATABASES, FACTUAL; PROTEIN CONFORMATION; PROTEIN STRUCTURE, TERTIARY; PROTEINS;

EID: 0032728082     PISSN: 10665277     EISSN: None     Source Type: Journal    
DOI: 10.1089/106652799318292     Document Type: Conference Paper

References (26)

1. Bernstein, F.C., Koetzle, T.F., Williams, G.J.B., Meyer, E.F., Brice, M.D., Rodgers, J.R., Kennard, O., Shimanouchi, T., and Tasumi, M. 1977. The protein data bank: A computer-based archival file for micromolecular structures. J. Mol. Bio. 112, 535-542.
2. Brown, N.P., Orengo, C.A., and Taylor, W.R. 1996. A protein structure comparison methodology. Computer Chem. 20, 359-380.
3. Creighton, T.E. 1992. Proteins: Structures and Molecular Properties. Freeman, San Francisco.
4. Fischer, D., Nussinov, R., and Wolfson, H. 1992. 3D substructure matching in protein molecules. Proc. 3rd Intl. Symp. Combinatorial Pattern Matching, Lecture Notes in Computer Science, 644, 459-477.
5. Golub, G.H., and Van Loan, C.F. 1996. Matrix Computations, 3rd ed. Johns Hopkins University Press, Baltimore.
6. Griendley, H.M., Artymiuk, P.J., Rice, D.W., and Willett, P. 1993. Identification of tertiary structure resemblance in proteins using a maximal common subgraph isomorphism algorithm. J. Mol. Biol. 229, 707-721.
7. Holm, L., and Sander, C. 1993. Protein structure comparison by alignment of distance matrices. J. Mol. Biol. 233, 123-138.
8. Holm, L., and Sander, C. 1994. Searching protein structure databases has come of age. Proteins: Struct. Funct. Genet. 19, 165-173.
9. Holm, L., and Sander, C. 1996. Mapping the protein universe. Science 273, 595.
10. 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. 38, 1-12.
11. Lesk, A.M. 1986. A toolkit for computational molecular biology II. On the optimal superposition of two sets of coordinates. Acta Crystallogr., A42 110-113.
12. Levitt, M. 1976. A simplified representation of protein conformations for the rapid simulation of protein folding. J. Mol. Biol. 104, 59-116.
13. Nishikawa, K., and Ooi, T. 1974. Comparison of homologous tertiary structures of proteins. J. Theoret. Biol. 43, 351-374.
14. Nishikawa, K., Momany, F., and Scheraga, H.A. 1974. Low-energy structures of two dipeptides and their relationship to bend conformations. Macromolecules 7, 797-806.
15. 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.
16. Pennec, X., and Ayache, N. 1998. A geometric algorithm to find small but highly similar 3D substructures in proteins. Bioinformatics 14, 516-522.
17. Rackovsky, S., and Scheraga, H.A. 1978. Differential geometry and polymer conformations 1. Comparison of protein conformations. Macromolecules 11, 1168-1174.
18. Rackovsky, S., and Scheraga, H.A. 1980. Differential geometry and polymer conformations 2. Development of a conformational distance function. Macromolecules 13, 1440-1453.
19. Rackovsky, S., and Goldstein, D.A. 1988. Protein comparison and classification: A differential geometry approach. Proc. Natl Acad. Sci. U.S.A 85, 777-781.
20. Rao, S.T., and Rossman, M.G. 1973. Comparison of super-secondary structures in proteins. Definition of general topological equivalence in protein structures. J. Mol. Biol. 76, 211-256.
21. Sali, A., and Blundell, T. 1990. J. Mol. Biol. 212, 403-428.
22. Srinivasan, R., Balasubramanian, R., and Rajan, S.S. 1975. Some new methods and general results of analysis of protein crystallographic structure data. J. Mol. Biol. 98, 739-747.
23. Taylor, W.R., ed. 1992. Patterns in Protein Sequence and Structure. Springer Series in Biophysics, Vol. 7, Springer-Verlag, Berlin.
24. Taylor, W.R., and Orengo, C.A. 1989. Protein structure alignment. J. Mol. Biol. 208, 1-22.
25. Vriend, G., and Sander, C. 1991. Detection of common three-dimensional substructures in proteins. Proteins: Struct. Funct. Genet. 11, 52-58.
26. Yee, D., and Dill, K. 1993. Families and the structural relatedness among globular proteins. Protein Sci. 2, 884-899.