PASSML: Combining evolutionary inference and protein secondary structure prediction

Bioinformatics

Volumn 14, Issue 8, 1998, Pages 726-733

  Liò, Pietro ^a   Goldman, Nick ^a   Thorne, Jeffrey L ^b   Jones, David T ^c  

^a UNIVERSITY OF CAMBRIDGE   (United Kingdom)

^b NORTH CAROLINA STATE UNIVERSITY   (United States)

^c UNIVERSITY OF WARWICK   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

AMINO ACID; PROTEIN;

ALGORITHM; AMINO ACID SEQUENCE; AMINO ACID SUBSTITUTION; ARTICLE; BIOLOGICAL MODEL; COMPUTER PROGRAM; DATA BASE; PHYLOGENY; PRIORITY JOURNAL; PROBABILITY; PROTEIN SECONDARY STRUCTURE;

EID: 0031788749     PISSN: 13674803     EISSN: 13674811     Source Type: Journal    
DOI: 10.1093/bioinformatics/14.8.726     Document Type: Article

References (31)

1. Adachi, J. and Hasegawa, M. (1995) MOLPHY: Programs for Molecular Phylogenetics Ver. 2.3. Institute of Statistical Mathematics, Tokyo.
2. Alber, T., Dao-pin, S., Nye, J.A., Muchmore, D.C. and Matthews, B.W. (1987) Temperature sensitive mutations of bacteriophage T4 lysozyme occur at sites with low mobility and low solvent accessibility in the folded protein. Biochemistry, 26, 3754-3758.
3. Asai, K., Hayamizu, S. and Handa, K. (1993) Prediction of protein secondary structure by the hidden Markov model. Comput. Applic. Biosci., 9, 141-146.
4. Benner, S.A., Badcoe, I., Cohen, M.A. and Gerloff, D.L. (1994) Bona fide prediction of aspects of protein conformation: assigning interior and surface residues from patterns of variation and conservation m homologous sequences. J. Mol. Biol., 235, 926-958.
5. Churchill, G.A. (1989) Stochastic models for heterogeneous DNA sequences. Bull. Math. Biol., 51, 79-94.
6. Dayhoff, M.O., Eck, R.V. and Park, C.M. (1972) A model of evolutionary change in proteins. In Dayhoff, M.O. (ed.), Atlas of Protein Sequence and Structure. National Biomedical Research Foundation, Washington, DC, Vol. 5, pp. 89-99.
7. Dayhoff, M.O., Schwartz, R.M. and Orcutt, B.C. (1978) A model of evolutionary change in proteins. In Dayhoff, M.O. (ed.), Atlas of Protein Sequence and Structure. National Biomedical Research Foundation, Washington, DC, Vol. 5, Suppl. 2, pp. 345-352.
8. Eddy, S. (1996) Hidden Markov models. Curr. Opin. Struct. Biol., 6, 361-365.
9. Felsenstein, J. (1981) Evolutionary trees from DNA sequences: a maximum likelihood approach. J. Mol. Evol., 17, 368-376.
10. Felsenstein, J. (1985) Phylogenies and the comparative method. Am. Nat., 125, 1-15.
11. Felsenstein, J. (1995) PHYLIP (Phylogenetic Inference Package) Ver. 3.57. Department of Genetics, University of Washington, Seattle.
12. Felsenstein, J. and Churchill, G.A. (1996) A hidden Markov model approach to variation among sites in rate of evolution. Mol Biol. Evol., 13, 93-104.
13. Goldman, N., Thorne, J.L. and Jones, D.T. (1996) Using evolutionary trees in protein secondary structure prediction and other comparative sequence analyses. J. Mol. Biol., 263, 196-208.
14. Goldman, N., Thorne, J.L. and Jones, D.T. (1998) Assessing the impact of secondary structure and solvent accessibility on protein evolution. Genetics, 149, 445-458.
15. Harvey, P.H., and Pagel, M.D. (1991) The Comparative Method in Evolutionary Biology. Oxford University Press, Oxford.
16. Hegvold, A.B. and Gabrielsen, O.S. (1997) The importance of the linker connecting the repeats of the c-Myb oncoprotein may be due to a positioning function. Nucleic Acids Res., 24, 3990-3995.
17. Heinz, D.W., Baase, W., Dahlquist, F.D. and Matthews, B.W. (1993) How amino acid insertions are allowed in an α-helix of T4 lysozyme. Nature, 361, 561-564.
18. Jones, D.T., Taylor, W.R. and Thornton, J.M. (1992) The rapid generation of mutation data matrices from protein sequences. Comput. Applic. Biosci., 8, 275-282.
19. Jones, D.T., Taylor, W.R. and Thornton, J.M. (1994) A mutation data matrix for transmembrane proteins. FEBS Lett., 339, 269-275.
20. Kabsch, W. and Sander, C. (1983) Dictionary of protein secondary structure: pattern recognition of hydrogen bonded and geometrical features. Biopolymers, 22, 2577-2637.
21. Lesk, A.M. and Chothia, C. (1982) Evolution of proteins formed by beta-sheets. II. The core of the immunoglobulin domains. J. Mol. Biol., 160, 325-342.
22. Mizuguchi, K. and Go, N. (1995) Comparison of spatial arrangements of the secondary structure elements in proteins. Protein Eng., 8, 353-362.
23. Omland, K.E. (1997) Correlated rates of molecular and morphological evolution. Evolution, 51, 1381-1393.
24. Rabiner, L.R. (1989) A tutorial on hidden Markov models and selected applications in speech recognition. Proc. IEEE, 77, 257-286.
25. Russell, R.B., Saqi, M.A.S., Sayle, R.A., Bates, P.A. and Sternberg, J.E. (1997) Recognition of analogous and homologous protein folds: analysis of sequence and structure conservation. J. Mol. Biol., 269, 423-439.
26. Thorne, J.L., Goldman, N. and Jones, D.T. (1996) Combining protein evolution and secondary structure. Mol. Biol. Evol., 13, 666-673.
27. Thornton, J.M., Sibanda, B.L., Edwards, M.S. and Barlow, D.J. (1988) Analysis, design and modification of loop regions in proteins. Bioessays, 8, 63-69.
28. Yang, Z. (1994) Maximum likelihood phylogenetic estimation from DNA sequences with variable rates over sites: approximate methods. J Mol. Evol., 39, 306-314.
29. Yang, Z. (1995) A space-time process model for the evolution of DNA sequences. Genetics, 139, 993-1005.
30. Yang, Z. (1996) Among-site rate variation and its impact on phylogenetic analysis. TREE, 11, 367-372.
31. Yang, Z., Goldman, N. and Friday, A. (1994) Comparison of models for nucleotide substitution used in maximum-likelihood phylogenetic estimation. Mol. Biol. Evol., 11, 316-324.