Global optimum protein threading with gapped alignment and empirical pair score functions

Journal of Molecular Biology

Volumn 255, Issue 4, 1996, Pages 641-665

  Lathrop, Richard H ^a,c   Smith, Temple F ^b  

^a MASSACHUSETTS INSTITUTE OF TECHNOLOGY   (United States)

^b Boston University   (United States)

^c UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

Amino acid pair potentials; Branch and bound search; Contact potentials; Protein folding; Protein structure prediction

Indexed keywords

ALGORITHM; AMINO ACID SEQUENCE; ARTICLE; COMPUTER ANALYSIS; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN FOLDING; SEQUENCE HOMOLOGY;

EID: 0029912991     PISSN: 00222836     EISSN: None     Source Type: Journal    
DOI: 10.1006/jmbi.1996.0053     Document Type: Article

References (70)

1. Abagyan, R., Frishman, D. & Argos, P. (1994). Recognition of distantly related proteins through energy calculations. Proteins: Struct. Func. Genet. 19, 132-140.
2. Aho, A. V., Hopcroft, J. E. & Ullman, J. D. (1982). Data Structures and Algorithms, Addison-Wesley, Reading, MA.
3. Altman, R. & Gerstein, M. (1994). Finding an average core structure: application to the globins. In Proceedings of the 2nd International Conference on Intelligent Systems for Molecular Biology (Altman, R., Brutlag, D., Karp, P., Lathrop, R. H. & Searls, D., eds), pp. 19-27, AAAI Press, Menlo Park, CA.
4. Bagley, S. C., Wei, L., Cheng, C. & Altman, R. B. (1995). Characterizing oriented protein structural sites using biochemical properties. In Proceedings of the 3rd International Conference on Intelligent Systems for Molecular Biology (Rawlings, C., Clark, D., Altman, R., Hunter, L., Lengauer, T. & Wodak, S., eds), pp. 12-20, AAAI Press, Menlo Park, CA.
5. Bashford, D., Chothia, C. & Lesk, A. M. (1987). Determinants of a protein fold: unique features of the globin amino acid sequences. J. Mol. Biol. 196, 199-216.
6. Bauer, A. & Beyer, A. (1994). An improved pair potential to recognize native protein folds. Proteins: Struct. Funct. Genet. 18, 254-261.
7. 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 macromolecular structures. J. Mol. Biol. 112, 535-542.
8. Bowie, F. U., Lüthy R. & Eisenberg, D. (1991). A method to identify protein sequences that fold into a known three-dimensional structure. Science, 253, 164-170.
9. Bowie, J. & Eisenberg, D. (1993). Inverted protein structure prediction. Curr. Opin. Struct. Biol. 3, 437-444.
10. Bryant, S. H. & Altschul, S. F. (1995). Statistics of sequence-structure threading. Curr. Opin. Struct. Biol. 5, 236-244.
11. Bryant, S. H. & Lawrence, C. E. (1993). An empirical energy function for threading protein sequence through the folding motif. Proteins: Struct. Funct. Genet. 16, 92-112.
12. Chothia, C. (1992). One thousand families for the molecular biologist. Nature, 357, 543-544.
13. Crippen, G. M. (1991). Prediction of protein folding from amino acid sequence over discrete conformational spaces. Biochemistry, 30, 4232-4237.
14. Eisenberg, D. & McLachlan, A. D. (1986). Solvation energy in protein folding and binding. Nature, 319, 199-203.
15. Eriksson, A. E., Cousens, L. S. & Matthews, B. W. (1993). Refinement of the structure of human basic fibroblast growth factor at 1.6 Å resolution and analysis of presumed heparin binding sites by selenate substitution. Protein Sci. 2, 1274-1284.
16. Fetrow, J. S. & Bryant, S. H. (1993). New programs for protein tertiary structure prediction. Bio/Technology, 11, 479-484.
17. Finkelstein, A. V. & Reva, B. (1991). A search for the most stable folds of protein chains. Nature, 351, 497-499.
18. Finzel, B. C., Poulos, T. L. & Kraut, J. (1984). Crystal structure of yeast cytochrome c peroxidase refined at 1.7 Å resolution. J. Biol. Chem. 259, 13027-13036.
19. Godzik, A., Kolinski, A. & Skolnick, J. (1992). Topology fingerprint approach to the inverse folding problem. J. Mol. Biol. 227, 227-238.
20. Goldstein, R. A., Luthey-Schulten, Z. A. & Wolynes, P. G. (1992). Tertiary structure recognition using optimized Hamiltonians with local interactions. Proc. Natl Acad. Sci. USA, 89, 9029-9033.
21. Greer, J. (1990). Comparative modeling methods: application to the family of the mammalian serine proteases. Proteins: Struct. Func. Genet. 7, 317-333.
22. Grossman, T., Farber, R. & Lapedes, A. (1995). Neural net representations of empirical protein potentials. In Proceedings of the 3rd International Conference on Intelligent Systems for Molecular Biology (Rawlings, C., Clark, D., Altman, R., Hunter, L., Lengauer, T. & Wodak, S., eds), pp. 154-161, AAAI Press, Menlo Park, CA.
23. Havel, T. F., Kuntz, I. D. & Crippen, G. M. (1983). The combinatorial distance geometry method for the calculation of molecular conformation. J. Theor. Biol. 104, 359-381.
24. Hendlich, M., Lackner, P., Weitckus, S., Floeckner, H., Froschauer, R., Gottsbacher, K., Casari, G. & Sippl, M. J. (1990). Identification of native protein folds amongst a large number of incorrect models: the calculation of low energy conformations from potentials of mean force. J. Mol. Biol. 216, 167-180.
25. Holm, L. & Sander, C. (1993). Protein structure comparison by alignment of distance matrices. J. Mol. Biol. 233, 123-138.
26. Holm, L. & Sander, C. (1994). The FSSP database of structurally aligned protein fold families. Nucl. Acids Res. 22, 3600-3609.
27. Johnson, M. S., Overington, J. P. & Blundell, T. L. (1993). Alignment and searching for common protein folds using a data bank of structural templates. J. Mol. Biol. 231, 735-752.
28. Jones, D. T. & Thornton, J. M. (1993). Protein fold recognition. J. Computer-Aided Mol. Design, 7, 439-456.
29. Jones, D. T., Taylor, W. R. & Thornton, J. M. (1992). A new approach to protein fold recognition, Nature, 358, 86-89.
30. Kabsch, W. & Sander, C. (1983). Dictionary of protein secondary structure. Biopolymers, 22, 2577-2637.
31. Karlin, S., Zuker, M. & Brocchieri, L. (1994). Measuring residue associations in protein structures: possible implications for protein folding. J. Mol. Biol. 239, 227-248.
32. Kavanaugh, J. S., Rogers, P. H. & Arnone, A. (1992). High-resolution X-ray study of deoxy recombinant human hemoglobins synthesized from beta-globins having mutated amino termini. Biochemistry, 31, 8640-8647.
33. Kumar, V. (1992). Search, branch-and-bound. In Encyclopedia of Artificial Intelligence (Shapiro, S. C., ed.), vol. 2, pp. 1468-1472, John Wiley & Sons, New York.
34. Lathrop, R. H. (1994). The protein threading problem with sequence amino acid interaction preferences is NP-complete. Protein Eng. 7, 1059-1068.
35. Lathrop, R. H. & Smith, T. F. (1994). A branch and bound algorithm for optimal protein threading with pairwise (contact potential) interaction preferences. In Proceedings of the 27th Hawaii International Conference on System Sciences (Hunter, L. & Shriver, B., eds), pp. 365-374, IEEE Computer Society Press, Los Alamitos, CA.
36. Lathrop, R. H., Webster, T. A. & Smith, T. F. (1987). ARIADNE: pattern-directed inference and hierarchical abstraction in protein structure recognition. Commun. ACM, 30, 909-921.
37. Lüthy R., Bowie, J. U. & Eisenberg, D. (1992). Assessment of protein models with three-dimensional profiles. Nature, 356, 83-85.
38. MacLachlan, R. A. (1992). Editor of CMU Common Lisp User's Manual. School of Computer Science, Carnegie Mellon University, Pittsburgh, PA. CMU Common Lisp source code and executables are freely available via anonymous FTP from lisp-rt1.slisp.cs.cmu.edu (128.2.217.9) and lisp-rt2.slisp.cs.cmu.edu (128.2.217. 10).
39. Maiorov, V. N. & Crippen, G. M. (1992). Contact potential that recognizes the correct folding of globular proteins. J. Mol. Biol. 227, 876-888.
40. Maiorov, V. N. & Crippen, G. M. (1994). Learning about protein folding via potential functions. Proteins: Struct. Funct. Genet. 20, 167-173.
41. Matsuo, Y. & Nishikawa, K. (1994). Protein structural similarities predicted by a sequence-structure compatibility method. Protein Sci. 3, 2055-2063.
42. Miyazawa, S. & Jernigan, R. L. (1985). Estimation of effective interresidue contact energies from protein crystal structures: quasi-chemical approximation. Macromolecules, 18, 534-552.
43. Moult, J., Pedersen, J. T., Judson, R. & Fidelis, K. (1995). A large-scale experiment to assess protein structure prediction methods. Proteins: Struct. Funct. Genet. 23, 2-4.
44. Novotný, J., Rashin, A. A. & Bruccoleri, R. E. (1988). Criteria that discriminate between native proteins and incorrectly folded models. Proteins: Struct. Funct. Genet. 4, 19-30.
45. Onesti, S., Brick, P. & Blow, D. M. (1991). Crystal structure of a Kunitz-type trypsin inhibitor from Erythrina caffra seeds. J. Mol. Biol. 217, 153-176.
46. Orengo, C. A. & Taylor, W. R. (1990). A rapid method of protein structure alignment. J. Theor. Biol. 147, 517-551.
47. Orengo, C. A., Jones, D. T. & Thornton, J. M. (1994). Protein superfamilies and domain superfolds. Nature, 372, 631-634.
48. Ouzounis, C., Sander, C., Scharf, M. & Schneider, R. (1993). Prediction of protein structure by evaluation of sequence-structure fitness. J. Mol. Biol. 232, 805-825.
49. Richardson, J. S. (1981). The anatomy and taxonomy of protein structures. Advan. Protein Chem. 34, 167-339.
50. Rost, B. & Sander, C. (1994). Conservation and prediction of solvent accessibility in protein families. Proteins: Struct. Funct. Genet. 20, 216-226.
51. Russell, R. B. & Barton, G. J. (1994). Structural features can be unconserved in proteins with similar folds. J. Mol. Biol. 244, 332-350.
52. Sander, C. & Schneider, R. (1991). Database of homolog-derived protein structures and the structural meaning of sequence alignment. Proteins: Struct. Funct. Genet. 9, 56-68.
53. Sankof, D. & Kruskal, J. B. (1983). Editors of Time Warps, String Edits and Macromolecules, Addison-Wesley, Reading, MA.
54. Sedgewick, R. (1990). Algorithms in C, Addison-Wesley, Reading, MA.
55. Shortle, D. (1995). Protein fold recognition. Nature Struct. Biol. 2, 91-93.
56. Sippl, M. J. (1990). Calculation of conformational ensembles from potentials of mean force: an approach to the knowledge-based prediction of local structures in globular proteins. J. Mol. Biol. 213, 859-883.
57. Sippl, M. J. (1993). Boltzmann's principle, knowledge-based mean fields and protein folding. J. Computer-Aided Mol. Design, 7, 473-501.
58. Sippl, M. J. (1995). Knowledge-based potentials for proteins. Curr. Opin. Struct. Biol. 5, 229-235.
59. Sippl, M. J. & Weitckus, S. (1992). Detection of native-like models for amino acid sequences of unknown three-dimensional structure in a data base of known protein conformations. Proteins: Struct. Funct. Genet. 13, 258-271.
60. Starzyk, R., Webster, T. & Schimmel, P. (1987). Evidence for disposable sequences inserted into a nucleotide fold. Science, 237, 1614-1618.
61. Steele, G. L. (1990). Common Lisp: the Language. Digital Press, Bedford, MA.
62. Stultz, C. M., Nambudripad, R., Lathrop, R. H. & White, J. V. (1995). Predicting protein structure with probabilistic models. In Protein Folding and Stability (Allewell, N. & Woodward, C., eds), JAI Press, Greenwich. In the press.
63. Taylor, W. R. & Orengo, C. A. (1989). Protein structure alignment. J. Mol. Biol. 208, 1-22.
64. Treharne, A. C., Ohlendorf, D. H., Weber, P. C., Wendoloski, J. J. & Salemme, F. R. (1990). X-ray structural studies of the cytokine interleukin 1-beta. Prog. Clin. Biol. Res. 349, 309-319.
65. Vainshtein, B. K., Harutyunyan, E. H., Kuranova, I. P., Borisov, V. V., Sosfenov, N. I., Pavlovsky A. G., Grebenko, A. I. & Konareva, N. V. (1975). Structure of leghaemoglobin from lupin root nodules at 5 Angstroms resolution. Nature, 254, 163-164.
66. Watson, H. C. (1969). The stereochemistry of the protein myoglobin. In Progress in Stereochemistry (Aylett, B. J. & Harris, M. M., eds), vol. 4, pp. 299-333, Butterworths, London.
67. White, J., Muchnik, I. & Smith, T. F. (1994). Modeling protein cores with Markov random fields. Math. Biosci. 124, 149-179.
68. Wilmanns, M. & Eisenberg, D. (1993). Three-dimensional profiles from residue-pair preferences: identification of sequences with β/α-barrel fold. Proc. Natl Acad. Sci. USA, 90, 1379-1383.
69. Winston, P. H. (1993). Artificial Intelligence, 3rd edit., pp. 82-90, Addison-Wesley, Reading, MA.
70. Wodak, S. J. & Rooman, M. J. (1993). Generating and testing protein folds. Curr. Opin. Struct. Biol. 3, 247-259.