Amino acid similarity matrix for homology modeling derived from structural alignment and optimized by the Monte Carlo method

Journal of Molecular Graphics and Modelling

Volumn 16, Issue 4-6, 1998, Pages 178-189

  Ogata, Koji ^a   Ohya, Masanori ^b   Umeyama, Hideaki ^a  

^a KITASATO UNIVERSITY   (Japan)

^b TOKYO UNIVERSITY OF SCIENCE   (Japan)

Author keywords

Amino acid similarity matrix; Information theory; Monte Carlo method; Probabilistic entropy; Sequence alignment; Structural alignment

Indexed keywords

AMINO ACID;

AMINO ACID ANALYSIS; AMINO ACID SEQUENCE; ARTICLE; ENTROPY; INFORMATION SCIENCE; MOLECULAR MODEL; PRIORITY JOURNAL; PROTEIN STRUCTURE; SEQUENCE ANALYSIS; STRUCTURE ANALYSIS; SYSTEM ANALYSIS; MODEL; SHORT SURVEY;

ALGORITHMS; AMINO ACID SEQUENCE; ENTROPY; IMMUNOPHILINS; MARKOV CHAINS; MOLECULAR SEQUENCE DATA; MONTE CARLO METHOD; PROBABILITY; PROTEIN STRUCTURE, TERTIARY; SEQUENCE ALIGNMENT; SEQUENCE HOMOLOGY, AMINO ACID; TACROLIMUS BINDING PROTEINS;

EID: 0032232531     PISSN: 10933263     EISSN: None     Source Type: Journal    
DOI: 10.1016/S1093-3263(99)00008-X     Document Type: Article

References (34)

1. 1 Greer, J. Comparative modeling methods: Application to the family of the mammalian serine proteases. Proteins, 1990, 7, 317-334.
2. 2 Matsuo, Y., and Nishikawa, K. Protein structural similarities predicted by a sequence-structure compatibility method. Protein Sci. 1994, 3, 2055-2063.
3. 3 Yoneda, T., Komooka, H., and Umeyama, H. A computer modeling study of the interaction between tissue factor pathway inhibitor and blood coagulation factor Xa. J. Protein Chem. 1997, 16, 597-605.
4. 4 Ogata, K., and Umeyama, H. The role played by environmental residues on side-chain torsional angles within homologous families of proteins: A new method of side-chain modeling. Proteins 1998, 31, 355-369.
5. 5 Needleman, S.B., and Wunsch, C.D. A general method applicable to the search for similarities in the amino acid sequence of two proteins. J. Mol. Biol. 1970, 48, 443-453.
6. 6 Sellers, P.H. On the theory and computation of evolutionary distance. SIAM J. Appl. Math. 1974, 26, 787-793.
7. 7 Smith, T.F., and Waterman, M.S. Identification of common molecular subsequences. J. Mol. Biol. 1981, 147, 195-197.
8. 8 Gotoh, O. An improved algorithm for matching biological sequences. J. Mol. Biol. 1982, 162, 705-708.
9. 9 Ohya, M., and Uesaka, Y. Amino acid sequences and DP matching. Inform. Sci. 1992, 63, 139-151.
10. 10 Miyazawa, S. A reliable sequence alignment method based on probabilities of residue correspondences. Protein Eng. 1994, 8, 999-1009.
11. 11 Taylor, W.R. An investigation of conservation-biased gap-penalties for multiple protein sequence alignment. Gene 1995, 165, GC27-GC35.
12. 12 Vogt, G., Ttzold, T., and Argos, P. An assessment of amino acid exchange matrices in aligning protein sequences: The twilight zone revisited. J. Mol. Biol. 1995, 249, 816-831.
13. 13 Gotoh, O. Significant improvement in accuracy of multiple protein sequence alignments by iterative refinement as assessed by reference to structure alignment. J. Mol. Biol. 1996, 264, 823-838.
14. 14 Taylor, W.R., and Orengo, C.A. Protein structure alignment. J. Mol. Biol. 1989, 208, 1-22.
15. 15 Sali, A., and Blundell, T.L. 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. 1990, 212, 403-442.
16. 16 Russell, R.B., and Barton, G.J. Multiple protein sequence alignment from tertiary structure comparison: Assignment of global and residue confidence levels. Proteins 1992, 14, 309-323.
17. 17 Gibrat, J.F., Madej, T., and Bryant, S.H. Surprising similarities in structure comparison. Curr. Opin. Struct. Biol. 1996, 6, 377-385.
18. 18 Holm, L., and Sander, C. Touring protein fold space with Dali/FSSP. Nucleic Acids Res. 1998, 26, 316-319.
19. 19 Toh, H. Introduction of a distance cut-off into structural alignment by the double dynamic programming algorithm. Comput. Appl. Biosci. 1997, 13, 387-396.
20. 20 Kanaoka, M., Kishimoto, F., Ueki, Y., and Umeyama, H. Alignment of protein sequences using the hydrophobic core scores. Protein Eng. 1989, 2, 347-351.
21. 21 Swindells, M.B. A procedure for the automatic determination of hydrophobia cores in protein structures. Protein Sci. 1995, 4, 93-102.
22. 22 Ohya, M., Miyazaki, S., and Ogata, K. On multiple alignment of genome sequences., IEICE Trans. Commun. 1992, E75-B, 453-457.
23. 23 Ishikawa, M., Toya, T., Hoshida, M., Nitta, K., Ogiwara, A., and Kanehisa, M. Multiple sequence alignment by parallel simulated annealing. Comput. Appl. Biosci. 1993, 9, 267-274.
24. 24 Notredame, C., and Higgins, D. SAGA: Sequence alignment by genetic algorithm. Nucleic Acids Res. 1996, 24, 1515-1524.
25. 25 Dayhoff, M.O., Schwartz, R.M., and Orcutt, B.C. A model of evolutionary change in proteins. In: Atlas of Protein Sequence and Structure (Dayhoff, M.O., ed.), Nat. Biomed. Res. Found., London, Vol. 5, Suppl. 3. 1978, pp. 345-352.
26. 26 Henikoff, S., and Henikoff, J.G. Amino acid substitution matrices from protein blocks. Proc. Natl. Acad. Sci. U.S.A. 1992, 89, 10915-10919.
27. 27 Gonnet, G.H., Cohen, M.A., and Benner, S.A. Exhaustive matching of the entire protein sequence database. Science 1992, 256, 1443-1445.
28. 28 Madej, T., Gibrat, J.F., and Bryant, S.H. Threading a database of protein cores. Proteins 1995, 23, 356-369.
29. 29 Ota, M., and Nishikawa, K. Assessment of pseudo-energy potentials by the best-five test: A new use of the three-dimensional profiles of proteins. Protein Eng. 1997, 10, 339-351.
30. 30 Chiu, T.L., and Goldstein, R.A. Optimizing energy potentials for success in protein tertiary structure prediction. Folding Design 1998, 3, 223-228.
31. 31 Risler, J.L., Delorme, M.O., Delacroix, H., and Henaut, A. Amino acid substitutions in structurally related proteins. A pattern recognition approach. J. Mol. Biol. 1988, 204, 1019-1029.
32. 32 Johnson, M.S., and Overington, J.P. A structural basis for sequence comparisons. An evaluation of scoring methodologies. J. Mol. Biol. 1993, 233, 716-738.
33. 33 Umegaki, H., and Ohya, M. Entropies in probabilistic systems. Kyoritsu Publishing Company, 1983.
34. 34 Bernstein, F.C., Koetzle, T.F., Williams, G.J.B., Meyer, E.F., Brice, M.D., Jr., Rodgers, J.R., Kennard, O., Shimanouchi, T., and Tasumi, M. The Protein Data Bank: A computer based archival file for micromolecular structures. J. Mol. Biol. 1977, 112, 535-542.