Identification of tertiary structure resemblance in proteins using a maximal common subgraph isomorphism algorithm

Journal of Molecular Biology

Volumn 229, Issue 3, 1993, Pages 707-721

  Grindley, Helen M ^a   Artymiuk, Peter J ^a   Rice, David W ^a   Willett, Peter ^a  

^a UNIVERSITY OF SHEFFIELD   (United Kingdom)

Author keywords

Database searching; Graph theory; Maximal common subgraph; Protein structure motif; Structural similarity

Indexed keywords

ALGORITHM; ARTICLE; COMPUTER PROGRAM; PRIORITY JOURNAL; PROTEIN CONFORMATION; PROTEIN STRUCTURE;

ALGORITHMS; AZURIN; CHYMOTRYPSIN; COMPUTER SIMULATION; HEAT-SHOCK PROTEINS; MODELS, MOLECULAR; PROTEIN STRUCTURE, TERTIARY; SOFTWARE; SUPPORT, NON-U.S. GOV'T; SUPPORT, U.S. GOV'T, NON-P.H.S.; THIOREDOXIN; UBIQUITINS; X-RAY DIFFRACTION;

EID: 0027511808     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1006/jmbi.1993.1074     Document Type: Article

References (73)

1. Abagyan, R. A. & Maiorov, V. N. (1988). A simple qualitative representation of polypeptide chain folds: comparison of protein tertiary structure. J. Biomol. Struct. Dynam. 5, 1267-1279.
2. Abagyan, R. A. & Maiorov, V. N. (1989). An automatic search for similar spatial arrangements of a-helices and /J-strands in globular proteins. J. Biomol. Struct. Dynam. 6, 1045-1060.
3. Abola, E. E., Bernstein, F. C., Bryant, S. H., Koetzle, T. F. & Weng, J. (1987). Protein Data Bank. In Crystallographic Databases: Information Content, Software Systems, Scientific Applications (Allen, F. H., Bergeroff, G. & Sievers, R., eds), pp. 107-132, Data Commission of the International Union of Crystallography, Cambridge.
4. Adman, E. T., Stenkamp, R. E., Sieker, L. C. & Jensen, L. H. (1978). A crystallographic model for azurin at 3 Â resolution. J. Mol. Biol. 123, 35-47.
5. Anymiuk, P. J., Mitchell, E. M., Rice, D. W. & Willett, P. (1989). Searching techniques for databases of protein structures. J. Inform. Sei. 15, 287-298.
6. Ar'ymiuk, P. J., Rice, D. W., Mitchell, E. M. & Willett, P. (1990). Structural resemblance between the families of bacterial signal transduction proteins and of G proteins revealed by graph theoretical techniques. Prot. Engin. 4, 39-43.
7. Artymiuk, P. J., Grindley, H. M., Mitchell, E. M., Rice, D. W., Ujah, E. C. & Willett, P. (1991). Searching techniques for tertiary structures of proteins in the Protein Data Bank. In Proceedings of the 1991 International Conference on Chemical Structures (Collier, H., ed.), pp. 91-106, Infonortics Ltd., Caine.
8. Artymiuk, P. J., Grindley, H. M., Park, J. E., Rice, D. W. & Willett, P. (1992). Three-dimensional structural resemblance between leucine aminopeptidase and carboxypeptidase A revealed by graph-theoretical techniques. FEBS Letters, 303, 48-52.
9. Ash, J. E., Warr, W. A. & Willett, P. (1991). Editors of Chemical Structure Systems, Ellis Horwood, Chichester.
10. Barlow, D. J. & Thornton, J. M. (1988). Helix geometry in proteins. J. Mol. Biol. 201, 601-619.
11. Barrow, H. G. & Burstall, R. M. (1976). Subgraph isomorphism, matching relational structures and maximal cliques. Inform. Proc. Letters, 4, 83-84.
12. Barrow, H. G. & Tenenbaum, J. M. (1981). Computational vision. Proc. IEEE, 69, 572-595.
13. Bernstein, F. C., Koetzle, T. F., Williams, G. J. B., Meyer, E. F., Brice, M. D., Rodgers, J. R., Kennard, O., Shimanouchi, T. & Tasumi, M. (1977). The Protein Data Bank: a computer-based archival file for macro-molecular structures. J. Mol. Biol. 112, 535-542.
14. Brint, A. T. & Willett, P. (1987). Algorithms for the identification of three-dimensional maximal common substructures. J. Chem. Inform. Comput. Sei. 27, 152-158.
15. Brint, A. T. & Willett, P. (1988). Upperbound procedures for the identification of similar three-dimensional chemical structures. J. Comput.-Aid. Mol. Des. 2, 311-320.
16. Brint, A. T., Davies, H. M., Mitchell, E. M. & Willett, P. (1989). Rapid geometric searching in protein structures. J. Mol. Graph. 7, 48-53.
17. Bron, C. & Kerbosch, J. (1973). Algorithm 457 - finding all cliques of an undirected graph. Commun. A.C.M. 16, 575-577.
18. Colman, P. M., Freeman, H. C., Guss, J. M., Murata, M., Norris, V. A., Ramshaw, J. A. M. & Ventakappa, M. P. (1978). X-ray crystal structure analysis of plastocyanin at 2-7 A resolution. Nature (London), 272, 319-324.
19. Crandcll, C. W. & Smith, D. H. (1983). Computcr assisted examination of compounds for common three-dimensional substructures. J. Chem. Inform. Comput. Sei. 23, 186-197.
20. Factor, A. D. & Mehler, E. L. (1991). Graphical representation of hydrogen bonding patterns in proteins. Protein Engin. 4, 421-425.
21. Flaherty, K. M., DeLuca-Flaherty, C. & McKay, D. B. (1990). Three-dimensional structure of the ATPase fragment of a 70 K heat-shock cognate protein. Nature (London), 346, 623-628.
22. Gati, G. (1979). Further annotated bibliography on the isomorphism disease. J. Graph Tkeor. 3, 95-109.
23. Ghose, A. K, & Crippen, G. M. (1985). Geometrically feasible binding modes of a flexible ligand molecule at the receptor-site. J. Comput. Chem. 6, 350-359.
24. Golender, V. & Rozenblit, A. (1983). Logical and Combinatorial Algorithms for Drug Design, Research Studies Press, Letchworth.
25. Grindley, H. M. (1991). The use of graph-theoretical techniques for searching databases of 3-D protein structures. Ph.D. Thesis, University of Sheffield.
26. Gronenborn, A. M. & Clore, G. M. (1989). Three-dimensional structures of proteins in solution by nuclear magnetic resonance spectroscopy. Protein Seq. Data Anal, 2, 1-8.
27. Havel, T. P. (1991). An evaluation of computational strategies for use in the determination of protein structure from distance constraints obtained by nuclear magnetic resonance. Prog. Biophys. Mol. Biol 56, 43-78.
28. Jakes, S. E., Watts, N. J., Willett, P., Bawden, D. & Fisher, J. D. (1987). Pharmacophoric pattern matching in files of chemical structures: evaluation of search performances. J. Mol Graph. 5, 41-48.
29. Jones, T. A. (1985). Interactive computer graphics: FRODO. Methods Enzymol. 115, 157-171.
30. Kabsch, W. (1976). A solution for the best rotation to relate two sets of vectors. Acta Crystallogr. Ser. A, 32, 922-923.
31. Kabsch, W. & S. Sander (1983). Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features. Biopolymers, 22, 2577-2637.
32. Karpen, M. E., deHaseth, P. L. & Neet, K. E. (1989). Comparing short protein substructures by a method based on backbone torsion angles. Proteins Struct. Fund. Genet. 6, 155-167.
33. Kraulis, P. (1991). Molscript: a program to produce both detailed and schematic plots of protein structures. J. Appl Crystallogr. 24, 946-950.
34. Kuhl, F. S., Crippen, G. M. & Friesen, D. K, (1984). A combinatorial algorithm for calculating ligand binding. J. Comput. Chem. 5, 24-34.
35. Ladenstein, R., Epp, O., Bartels, K., Jones, A., Huber, R. & Wendel, A. (1979). Structure analysis and molecular model of the selenoenzyme glutathione peroxidase at 2-8 A resolution. J. Mol. Biol. 134, 199-218.
36. Lathrop, R. H., Webster, T. H. & Smith, T. F. (1987). ARIADNE: pattern-directed inference and hierarchical abstraction in protein structure recognition, Commun. A.C.M. 30, 909-921.
37. Levi, G. (1972). A note on the derivation of maximal common subgraphs of two directed or undirected graphs. Calcolo, 9, 341-352.
38. Levine, M., Stuart, D. & Williams, J. (1984). A method for the systematic comparison of the three-dimensional structures of proteins and some results. Acta Crystallogr. Ser. A, 40, 600-610.
39. Liu, Z. J. & van Rapenbusch, R. (1989). A fast system for the best matching of two sets of atomic coordinates. Comput. Chem. 13, 5-23.
40. Martin, Y. C., Bures, M. G. & Willett, P. (1990). Searching databases of three-dimensional structures. In Reviews in Computational Chemistry (Lipkowitz, K. B. & Boyd, D. B., eds), pp. 213-263, VCH, New York.
41. McGregor, J. J. (1982). Backtrack search algorithms and the maximal common subgraph problem. Software Prad. Exper. 12, 23-34.
42. McLachlan, A. D. (1972). A mathematical procedure for superimposing atomic coordinates of proteins. Acta Crystallogr. Ser. A, 28, 656-657.
43. McLachlan, A. D. (1979). Gene duplication in the structural evolution of Chymotrypsin. J. Mol. Biol. 128, 49-79.
44. Mitchell, E. M., Artymiuk, P. J., Rice, D. W. & Willett, P. (1990). Use of techniques derived from graph theory to compare secondary structu re motifs in proteins. J. Mol Biol. 212, 151-166.
45. Murthv, M. R. N. (1984). A fast method of comparing protein structures. FEBS Letters, 168, 97-102.
46. Needleman, S. B. & Wunsch, C. D. (1970). A general method applicable to the search for similarities in the amino-acid sequence of two proteins. J. Mol. Biol 48, 443-453.
47. Nishikawa, K. & Ooi, T. (1974), Comparison of homologous tertiary structures of proteins. J. Theoret. Biol. 43, 351-374.
48. Nishikawa, K., Ooi, T., Isagai, Y. & Saito, N. (1972). Tertiary structure of proteins. I. Representation and computation of the conformations. J. Phys. Soc. Japan, 32, 1331-1337.
49. Nussinov, R. (1987). Theoretical molecular biology: prospectives and perspectives. J. Theoret. Biol 125, 219-235.
50. Pepperrell, C. M. & Willett, P. (1991). Techniques for the calculation of 3-dimensional structural similarity using inter-atomic distances. J. Comput.-Aid. Mol. Des. 5, 455-476.
51. Phillips, D, C. (1970). British biochemistry past and present. Biockem. Soc. Symp. no. 31, 11-28.
52. Rao, S. T. & Rossmann, M. G. (1973). Comparison of super-secondary structures in proteins. J. Mol. Biol. 76, 241-256.
53. Rawlings, C. J., Taylor, W. R., Nyakairu, J., Fox, J. & Sternberg, M. J. E. (1985). Reasoning about protein topology using the logic programming language PROLOG. J. Mol. Graph. 3, 151-157.
54. Read, R. C. & Corneil, D. G. (1977). The graph isomorphism disease. J. Graph Theor. 1, 339-363.
55. Reinemer, P., Dirr, H. W., Ladenstein, R., Schaffer, J., Gallay, O. & Huber, R. (1991). The three-dimensional structure of class % glutathione S-transferase in complex with glutathione sulfonate at 2 3 A resolution. EM BO J. 10, 1997-2005.
56. Remington, S. J. & Matthews, B. W. (1978). A general method to assess similarity of proteins with applications to T4 bacteriophage lysozyme. Proc. Nat. Acad. Sei., U.S.A. 75, 2180-2184.
57. Richards, M. & Kundrot, C. E. (1988). Identification of structural motifs from protein coordinate data: secondary structure and first-level supersecondary structure. Proteins Struct. Fund. Genet. 3, 71-84.
58. Richardson, J. S. (1977). J-sheet topology and the relatedness of proteins. Nature (London), 268, 495-500.
59. Richardson, J. S. (1981). The anatomy and taxonomy of protein structure. Advan. Prot. Chem. 34, 167-339.
60. Rossmann, M. G. & Argos, P. (1981). Protein folding. Annu. Rev. Biochem. 50, 497-532.
61. Ryden, L. & Lundgren, J.-O. (1976). Homologous relationships among the small blue proteins. Nature (London), 261, 344-346.
62. Sali, A. & Blundell, T. L. (1990). Definition of general topological equivalence in protein structures: a procedure involving comparison of properties and relationships through simulated annealing and dynamic programming. J. Mol Biol. 212, 403-428.
63. Sheridan, R. P., Dixon, J. S. & Venkataraghavan, R. (1985). Generating plausible protein folds by secondary structure similarity. Int. J. Pept. Protein Res. 25, 132-143.
64. Sheridan, R. P., Nilakantan, R., Rusinko, A., Bauman, N., Haraki, K. S. & Venkataraghavan, R. (1989). 3DSEARCH: a system for three-dimensional substructure searching. J. Chem. Inform. Comput. Sei. 29, 255-260.
65. Subbarao, N. & Haneef, I. (1991). Defining topological equivalences in macromolecules. Protein Engin. 4, 877-884.
66. Takahashi, Y., Maeda, S. & Sasaki, S.-I. (1987). Automated recognition of common geometrical patterns among a variety of three-dimensional molecular structures. Anal. Chim. Acta, 200, 363-377.
67. Tajlor, W. R. & Orengo, C. A. (1989). Protein structure alignment. J. Mol. Biol. 208, 1-22.
68. Van Drie, J. H., Weininger, D. & Martin, Y C. (1989). ALADDIN - an integrated tool for computer-assisted molecular design and pharmacophore recognition from geometric, steric and substructure searching of 3-dimensional molecules. J. Comput.-Aid. Mol. Des. 3, 225-251.
69. Vriend, G. & Sander, C. (1991). Detection of common three-dimensional substructures in proteins. Proteins Struct. Funct. Genet. 11, 52-58.
70. Waterman, M. S. (1984). General methods of sequence comparison. Bull. Math. Biol. 46, 473-500.
71. Willett, P. (1991). Three-dimensional Chemical Structure Handling, Research Studies Press, Taunton.
72. Wuthrich, K. (1986). NMR of Proteins and Nucleic Acids, Wiley-Interscience, New York.
73. Zuker, M. & Somorjai, R. L. (1989). The alignment of protein structures in three dimensions. Bull. Math. Biol. 51, 55-78.