Detection of distant structural similarities in a set of proteins using a fast graph-based method

Proceedings of the 5th International Conference on Intelligent Systems for Molecular Biology, ISMB 1997

Volumn , Issue , 1997, Pages 167-178

  Koch, Ina ^a,b   Lengauer, Thomas ^b,c  

^a Center for Information Technology ^*  (Germany)

^b FRAUNHOFER INSTITUTE FOR APPLIED INFORMATION TECHNOLOGY FIT   (Germany)

^c UNIVERSITY OF BONN   (Germany)

Author keywords

graph algorithm; maximal common subgraph; multiple structure eilignment; structural similar

Indexed keywords

GRAPH THEORY; GRAPHIC METHODS; PROBLEM SOLVING;

COMMON SUBGRAPH; GRAPH ALGORITHMS; GRAPH-BASED METHODS; MAXIMAL COMMON SUBGRAPH; MULTIPLE STRUCTURE EILIGNMENT; MULTIPLE STRUCTURES; PROTEINS STRUCTURES; STRUCTURAL SIMILAR-; STRUCTURAL SIMILARITY; SUBGRAPH PROBLEMS;

PROTEINS;

BACTERIAL PROTEIN; BACTERIOCHLOROPHYLL; BIRA PROTEIN, E COLI; DNA DIRECTED DNA POLYMERASE GAMMA; ESCHERICHIA COLI PROTEIN; LIGASE; PHOSPHATASE; PORIN; REPRESSOR PROTEIN; TRANSCRIPTION FACTOR;

ALGORITHM; ARTICLE; CHEMICAL MODEL; CHEMICAL STRUCTURE; CHEMISTRY; COMPARATIVE STUDY; COMPUTER SIMULATION; FACTUAL DATABASE; GENETICS; METHODOLOGY; PROTEIN CONFORMATION; PROTEIN SECONDARY STRUCTURE; SEQUENCE ALIGNMENT; STATISTICS;

ALGORITHMS; BACTERIAL PROTEINS; BACTERIOCHLOROPHYLLS; CARBON-NITROGEN LIGASES; COMPUTER SIMULATION; DATABASES, FACTUAL; DNA POLYMERASE III; ESCHERICHIA COLI PROTEINS; MODELS, CHEMICAL; MODELS, MOLECULAR; PHOSPHORIC MONOESTER HYDROLASES; PORINS; PROTEIN CONFORMATION; PROTEIN STRUCTURE, SECONDARY; REPRESSOR PROTEINS; SEQUENCE ALIGNMENT; TRANSCRIPTION FACTORS;

EID: 0030629298     PISSN: None     EISSN: None     Source Type: Conference Proceeding    
DOI: None     Document Type: Conference Paper

References (32)

1. Alexandrov, N., and Fischer, D. 1996. Analysis of topological and nontopological structural similarities in the PDB: new examples with old structures. PROTEINS: Structure, Function, and Genetics 25:354-365.
2. Artymiuk, P.; Rice, D.; Mitchell, E.; and P. Willett, P. 1990. Structural resemblance between the families of bacterial signal-transduction proteins and of
3. G proteins revealed by graph theoretical techniques. Protein Engineering 4:39-43.
4. Bachar, 0.; Fischer, D.; R. Nussinov, R.; and H. Wolf-son, H. 1993. A computer vision based for 3-d sequence-independent structural comparison of proteins. Protein Engineering 6:279-288.
5. Bernstein, F.; Koetzle, T.; Williams, G.; Meyer, Jr., E.; Brice, M.; Rodgers, J.; Kennard, O.; Shi-manouchi. T.; and Tasumi, M. 1977. The protein data bank: a computer based archival file for macro-molecular structures. J.Mol.Biol. 112:535-542.
6. Brint, A., and Willett, P. 1987. Pharmacophoric pattern matching in files of 3D chemical structures: comparision of geometric searching algorithms. J.Mol.Graphics 5:49-56.
7. Bron, C., and Kerbosch, J. 1973. Algorithm 457 - finding all cliques of an imdirected graph. Com-mun.ACM 16:575-577.
8. Fciuman, E., and Saper, M. 1996. Structure and function of the protein tyrosine phosphatases. Trends in Biochem.Sci. 21:413-17.
9. Grindley, H.; Artymiuk, P.; Rice, D.; and Willett, P. 1993. Identification of tertiary structure resemblance in proteins using a maximal common subgraph isomorphism algorithm. J.Mol.Biol. 229:707-721.
10. Gusfield, D.; Balasubramanian, K.; and Naor, D. 1992. Parametric optimization of sequence alignment. In Proceedings of the Third Annual ACM-SIAM Symposium on Discrete Algorithms, 432-39.
11. Holm, L., and Sander, C. 1993. Protem structure comparison by alignment of distance matrices. J.Mol.Biol. 233:123-138.
12. Holm, L., and Sander, C. 1995. 3-D-lookup: Fast protein struckture database searches at 90% reliability. In Rawlings, C; Clark, D.; Altman, R.; Hunter, L.; Lengauer, T.; and Wodak, S., eds., Proceedings Third International Conference on Intelligent Systems for Molecular Biology. Menlo Pćirk, California: AAAI Press. 179-187.
13. Johnson, M.; Sali, A.; and Blundell, T. 1990. Phylo-genetic relationships from three-dimensional protein structures. Methods in Enzym. 183:670-690.
14. Kabsch, W., and Sander, C. 1983. Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded ćmd geometrical features. Biopoly-mers 22:2577-2637.
15. Kaden, F.; Koch, I.; and Selbig, J. 1990. Knowledge-based prediction of protein structures. J.theor.Biol. 147:85-100.
16. Koch, I.; Kaden, F.; and Selbig, J. 1992. Analysis of protein sheet topologies by graph-theoretical methods. PROTEINS: Structure, Function, and Genetics 12:314-323.
17. Koch, L; Lengauer, T.; and Wanke, E. 1996. An algorithm for finding maximal common subtopologies in a set of protein structures. J.Comp.Biol. 3:289-306.
18. Lathrop, R.; Webster, T.; and Smith, T. 1987. ARIADNE: pattern-directed inference and hierarchical abstraction in protein structure recognition. Com-mun.yl CM 30:909-921.
19. Lessel, U., and Schomburg, D. 1994. Similarities between protein 3-D structures. Protein Engineering 7:1175-1187.
20. May, A., and Johnson, M. 1994. Protein structure comparisons using a combination of a genetic algorithm, dynamic programming and least-squares minimization. Protein Engineering 7:475-485.
21. Mitchell, E.; Artymiuk, P.; Rice, D.; and Willett, P. 1993. Use of techniques derived from graph theory to compare secondary structure motifs in proteins. J.Mol.Biol. 212:151 166.
22. Mizuguchi, K., and Go, N. 1995. Comparison of spatial arrangements of secondćiry structural elements in proteins. Protein Engineering 8:353-362.
23. Needleman, S., aind Wunsch, C. 1970. A general method applicable to the search for similarities in the amino acid sequence of two proteins. J.Mol.Biol. 48:443-453.
24. Orengo, C; Brown, N.; and Taylor, W. 1992. Fast structure alignment for protein databank searching. PROTEINS: Structure, Function, and Genetics 14:139-167.
25. Pickett, S.; Saqi, M.; and Sternberg, M. 1992. Evaluation of the sequence template method for protein structure prediction. J.Mol.Biol. 228:170-187.
26. Rufino, S., and Blundell, T. 1994. Structure-based identification and clustering of protein families and superfamilies. J.Comp.-Aid.Mol.Design 8:5-27.
27. Sayle, R. 1996. RasMol Molecular Graphics Visualisation Tool. Glaxo Research & Development, Green-ford, Middlesex Version 2.5.
28. Sutcliffe, M.; Haneef, I.; Carney, D.; and Blundell, T. 1987. Knowledge based modelling of homologous proteins, pćirt I: three-dimensional frameworks derived from the simultaneous superposition of multiple structures. Protein Engineering 1:377-384.
29. Taylor, W., and Orengo, C. 1996. Protein structure alignment. J.Mol.Biol. 208:1-22.
30. Taylor, W.; Flores, T.; and Orengo, C. 1994. Multiple protein structure alignment. Protein Science 3:1858-1870.
31. Sali, A., and Blundell, T. 1990. Definition of general topological equivéïlence in protein structures: a procedure involving comparison of properties ćmd relationships through simulated annećiling and dynamic programming technique. J.Mol.Biol. 212:344-346.
32. Waterman, M.; Eggert, M.; and Lunder, E. 1992. Parametric sequence comparisons. Proc.Nat.Acad.Sci.USA 89:6090-6093.