The art of matchmaking: Sequence alignment methods and their structural implications

Structure

Volumn 7, Issue 1, 1999, Pages

  Smith, Temple F ^a  

^a Boston University   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

DNA;

AMINO ACID SEQUENCE; GENE STRUCTURE; GENETIC PROCEDURES; HUMAN; MOLECULAR DYNAMICS; PRIORITY JOURNAL; PROTEIN STRUCTURE; REVIEW; SEQUENCE ANALYSIS; SEQUENCE HOMOLOGY; STRUCTURE ANALYSIS;

EID: 0033555420     PISSN: 09692126     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0969-2126(99)80003-3     Document Type: Note

References (41)

1. Chervitz, S.A., et al., & Botstein, D. (1998). Comparison of the complete protein sets of worm and yeast: Orthology and divergence. Science 282, 2022-2028.
2. Mewes, H.W., et al., & Zollner, A. (1997). Overview of the yeast genome. Nature, 387, 7-65. [Published erratum appears in Nature 387, p. 737.]
3. Kendrew, J.C. (1958). The three-dimensional structure of a myoglobin. Nature 181, 662-666.
4. Zuckerkandl, E. & Pauling, L.C. (1965). Molecules as documents of evolutionary history. J. Theoret. Biol. 8, 357-358.
5. Dayhoff, M.O. & Eck, R.V. (1966). Atlas of Protein Sequence and Structure. Volume 2, NBRF Press, Silver Spring, MD.
6. 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.
7. Smith, T.F. & Waterman, M.S. (1981). Identification of common molecular subsequences. J. Mol. Biol. 147, 195-197.
8. Altschul, S.F., Gish, W., Miller, W., Myers, E.W. & Lipman, D.J. (1990). Basic local alignment search tool. J. Mol. Biol. 215, 403-410.
9. Waterman, M.S., Smith, T.F. & Beyer, W.A. (1976). Some biological sequence metrics. Adv. Mathematics 20, 367-387.
10. Feldmann, R.J., et al., & Caporale, L.H. (1985). On the construction of computer models of proteins by the extension of crystallographic structures. Ann. NY Acad. Sci. 439, 12-43.
11. Greer, J. (1990). Comparative modeling methods: Application to the family of the mammalian serine proteases. Proteins 7, 317-334.
12. Lathrop, R.H. & Smith, T.F. (1996). Global optimum protein threading with gapped alignment and empirical pair score functions. J. Mol. Biol. 255, 641-665.
13. Taylor, W.R. (1997). Multiple sequence threading: An analysis of alignment quality and stability. J. Mol. Biol. 269, 902-943.
14. Pearson, W.R. & Lipman, D.J. (1988). Improved tools for biological sequence comparison. Proc. Natl Acad. Sci. USA 85, 2444-2448.
15. Henikoff, S. & Henikoff, J.G. (1992). Amino acid substitution matrices from protein blocks. Proc. Natl Acad. Sci. USA 89, 10915-10919.
16. Karlin, S. & Altschul, S.F. (1990). Methods for assessing the statistical significance of molecular sequence features by using general scoring schemes. Proc. Natl Acad. Sci. USA 87, 2264-2268.
17. Feng, D.F. & Doolittle, R.F. (1987). Progressive sequence alignment as a prerequisite to correct phylogenetic trees. J. Mol. Evol. 25, 351-360.
18. Smith, R.F. & Smith, T.F. (1990). Automatic generation of primary sequence patterns from sets of related protein sequences. Proc. Natl Acad. Sci. USA 87, 118-122.
19. Gotoh, O. (1982). An improved algorithm for matching biological sequences. J. Mol. Biol. 162, 705-708.
20. Smith, T.F., Lathrop, R.H. & Cohen, F. (1996). The identification of protein functional patterns. In Integrative Approaches to Molecular Biology. (Collado-Vides, J., Magasanik, B. & Smith T.F., eds.), MIT Press, Cambridge, MA.
21. Bork, P. & Koonin, E.V. (1996). Protein sequence motifs. Curr. Opin. Struct. Biol. 6, 366-376.
22. Bairoch, A. (1992). PROSITE: A dictionary of sites and patterns in proteins. Nucleic Acids Res. 20, 2013-2018.
23. Sonnhammer, E.L., Eddy, S.R. & Durbin, R. (1997). Plam: A comprehensive database of protein domain families based on seed alignments. Proteins 28, 405-420.
24. Adams, R.M., Das, S. & Smith, T.F. (1996). Multiple domain protein diagnostic patterns. Protein Sci. 5, 1240-1249.
25. Gracy, J. & Argos, P. (1998). Automated protein sequence database classification. II. Delineation of domain boundaries from sequence similarities. Bioinformatics 14, 174-187.
26. Zhang, X. & Smith, T.F. (1998). Yeast operons. Microb. Comput. Gen. 3, 133-140.
27. Altschul, S.F., et al., & Lipman, D.J. (1997). Gapped BLAST and PSI- BLAST: A new generation of protein database search programs. Nucleic Acids Res. 25, 3389-3402.
28. Rost, B. & Sander, C. (1993). Prediction of protein secondary structure at better than 70% accuracy. J. Mol. Biol. 232, 584-599.
29. Eisenberg, D., Wilcox, W. & Eshita, S. (1987). Hydrophobie moments as tools for analysis of protein sequences. In Proteins: Structure and Function. (L'Italien, JJ., ed.), pp. 425-436, Plenum Press, New York.
30. Waterman, M.S. (1983). Sequence alignments in the neighborhood of the optimum with general applications to dynamic programming. Proc. Natl Acad. Sci. USA 80, 2132-3124.
31. Zhu, J., Liu, J.S. & Lawrence, C.E. (1998). Bayesian adaptive sequence alignment algorithms. Bioinformatics 14, 25-39.
32. Chothia, C. & Lesk, A.M. (1986). The relation between the divergence of sequence and structure in proteins. EMBO J. 5, 823-826.
33. Matthews, B.W. & Rossmann, M.G. (1985). Comparison of protein structures. Methods Enzymol. 115, 397-420.
34. Bowie, F.U. & Eisenberg, D. (1993). Inverted protein structure prediction. Curr. Opin. Struct. Biol. 3, 437-444.
35. Miyazawa, S. & Jernigan, R.L. (1985). Estimation of effective interresidue contact energies from protein crystal structures: Quasi-chemical approximation. Macromolecules 18, 534-552.
36. Smith, T.F., Lo Conte, L., Bienkowska, J., Gaitatzes, C., Rogers, R.J. & Lathrop, R. (1997). Current limitations to protein threading approaches. J. Comput. Biol. 4, 217-225.
37. Lathrop, R.H. (1994). The protein threading problem with sequence amino acid interaction preferences is NP-complete. Protein Eng. 7, 1059-1068.
38. Xu, Y., Xu, D. & Uberbacher, E.C. (1998). An efficient computational method for globally optimal threading. J. Comput. Biol. 5, 597-614.
39. Rabiner, L.R. (1989). A tutorial on hidden Markov models and selected applications in speech recognition. Proc. IEEE 77, 257-286.
40. White, J.V. (1988). Modeling and filtering for discretely valued time series. In Bayesian Analysis of Time Series and Dynamic Models. (Spall J.C., ed.), Marcel Dekker, New York.
41. Yu, L., White, J.V. & Smith, T.F. (1998). A homology identification method that combines protein sequence and structure information. Protein Sci. 7, 2499-2510.