FORESST: Fold recognition from secondary structure predictions of proteins

Bioinformatics

Volumn 15, Issue 2, 1999, Pages 131-140

  Di Francesco, V ^a,b   Munson, P J ^a   Garnier, J ^a,c  

^a Department of Electrical Engineering   (United States)

^b J CRAIG VENTER INSTITUTE   (United States)

^c CEMAGREF   (France)

Author keywords

[No Author keywords available]

Indexed keywords

POLYPEPTIDE; PROTEIN;

AMINO ACID SEQUENCE; ARTICLE; COMPUTER MODEL; CONTROLLED STUDY; DATA BASE; METHODOLOGY; MOLECULAR MODEL; PREDICTION; PRIORITY JOURNAL; PROTEIN FAMILY; PROTEIN FOLDING; PROTEIN SECONDARY STRUCTURE;

EID: 0032972348     PISSN: 13674803     EISSN: 13674811     Source Type: Journal    
DOI: 10.1093/bioinformatics/15.2.131     Document Type: Article

References (41)

1. Altschul, S.F., Gish, W., Miller, W., Myers, E.W. and Lipman, D.J. (1990) Basic local alignment search tool. J. Mol. Biol., 215, 403-410.
2. Barrett, C., Hughey, R. and Karplus, K. (1997) Scoring hidden Markov models. Comput. Applic. Biosci., 13, 191-199.
3. Bernstein, F.C., Koetzle, T.F., Williams, G.J.B., Meyer, E.F., Brice, M.D., Rodgers, J.R., Kennard, O., Shimanovichi, T. and Tasumi, M. (1977) The Protein Data Bank: a computer-based archival file for macromolecular structures. J. Mol. Biol., 112, 535-542.
4. Browne, W.J., North, A.C.T., Phillips, D.C., Brew, K., Vanaman, T.C. and Hill, R.L. (1969) A possible three-dimensional structure of bovine α-lactalbumin based on that of hen's egg-white lysozyme. J. Mol. Biol., 42, 65-86.
5. Bryant, S.H. (1996) Evaluation of threading specificity and accuracy. Proteins: Struct. Funct. Genet., 26, 172-185.
6. Chothia, C. and Lesk, A.M. (1986) The relation between the divergence of sequence and structure in proteins. EMBO J., 5, 823-826.
7. Di Francesco, V., Garnier, J. and Munson, P.J. (1997a) Protein topology recognition from secondary structure sequences - Application of the hidden Markov models to the alpha class proteins. J. Mol. Biol., 267, 446-463.
8. Di Francesco, V., Geetha, V., Garnier, J. and Munson, P.J. (1997b) Fold recognition using predicted secondary structure sequences and hidden Markov models of protein folds. Proteins: Struct. Funct. Genet. Suppl., 1, 123-128.
9. Di Francesco, V., McQueen, P., Garnier, J. and Munson, P.J. (1997c) Incorporating global information into secondary structure prediction with hidden Markov models of protein folds. In Proceedings of the 5th International Conference on Intelligent Systems in Molecular Biology, pp. 100-103. AAAI Press, Menlo Park, CA.
10. Doolittle, R.F. (1992) Stein and Moore Award address. Reconstructing history with amino acid sequences. Protein Sci., 1, 191-200.
11. Fischer, D. and Eisenberg, D. (1996) Protein fold recognition using sequence-derived predictions. Protein Sci., 5, 947-955.
12. Frishman, D. and Argos, P. (1996) Incorporation of non-local interactions in protein secondary structure prediction from the amino acid sequence. Protein Eng., 9, 133-142.
13. Garnier, J., Gibrat, J.-F. and Robson, B. (1996) GOR method for predicting protein secondary structure from amino acid sequence. Methods Enzymol., 266, 540-553.
14. Greer, J. (1991) Comparative modeling in homologous proteins. Methods Enzymol., 202, 239-252.
15. Hogg, R.V. and Craig, A.T. (1978) Introduction to Mathematical Statistics. Macmillan, New York.
16. Hubbard, T.J. and Park, J. (1995) Fold recognition and ab initio structure predictions using hidden Markov models and β-strand pair potential. Proteins: Struct. Funct. Genet., 23, 398-402.
17. Hughey, R. and Krogh, A. (1995) SAM: Sequence alignment and modeling software system. Technical Report. UCSC-CRL-95-7. University of California, Santa Cruz, CA.
18. Jones, D. and Thornton, J. (1993) Protein fold recognition. J. Comput. Aided Mol. Des., 7, 439-456.
19. Kabsch, W. and Sander, C. (1983) Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features. Biopolymers, 22, 2577-2637.
20. Kline, A.D. et al. (1997) Leptin is a four-helix bundle: secondary structure by NMR. FEBS Lett., 407, 239-242.
21. Krogh, A., Brown, M., Mian, I.S., Sjolander, K. and Haussler, D. (1994) Hidden Markov models in computational biology: Applications to protein modeling. J. Mol. Biol., 235, 1501-1531.
22. Lemer, C.M.-R., Rooman, M.J. and Wodak, S.J. (1995) Protein structure prediction by threading methods: evaluation of current techniques. Proteins: Struct. Funct. Genet., 23, 337-355.
23. Levin, J.M. and Garnier, J. (1988) Improvements in secondary structure prediction method based on search for local sequence homologies and its use as a model building tool. Biochim. Biophys. Acta, 955, 283-295.
24. Levitt, M. (1997) Competitive assessment of protein fold recognition and alignment accuracy. Proteins: Struct. Funct. Genet. Suppl., 1, 92-104.
25. Marchler-Bauer, A., Levitt, M. and Bryant, S.H. (1997) A retrospective analysis of CASP2 threading predictions. Proteins: Struct. Funct. Genet. Suppl., 1, 83-91.
26. Munson, P.J., Di Francesco, V. and Porrelli, R.N. (1994) Protein secondary structure prediction using periodic-quadratic-logistic models: statistical and technical issues. In Proceedings of the 27th Hawaii Int. Conf. Sys. Sci. IEEE Press, Los Alamitos. CA. Vol. V. pp. 375-384.
27. Murzin, A.G., Brenner, S.E., Hubbard, T. and Chothia, C. (1995) SCOP: a structural classification of proteins database for the investigation of sequences and structures. J. Mol. Biol., 247, 536-540.
28. Orengo, C.A., Flores, T.P., Taylor, W.R. and Thornton, J.M. (1993) Identification and classification of protein fold families. Protein Eng., 6, 485-500.
29. Orengo, C.A., Jones, D.T. and Thornton, J.M. (1994) Protein superfamilies and domain superfolds. Nature, 372, 631-634.
30. Pearson, W.R. (1996) Effective protein sequence comparison. Methods Enzymol., 266, 227-258.
31. Rabiner, L.R. (1989) A tutorial on hidden Markov models and selected applications in speech recognition. Proc. IEEE, 77, 257-286.
32. Rice, D.W. and Eisenberg, D. (1997) A 3D-1D substitution matrix for protein fold recognition that included predicted secondary structure of the sequence. J. Mol. Biol., 267, 1026-1038.
33. Richardson, J.S. (1981) The anatomy and taxonomy of protein structure. Adv. Protein Chem., 34, 167-339.
34. Robson, B. and Garnier, J. (1986) Introduction to Proteins and Protein Engineering. Elsevier Science, Amsterdam.
35. Rost, B. (1995) TOPITS: Threading One-dimensional Predictions Into Three-dimensional Structures. In Proceedings of the 3rd International Conference on Intelligent Systems in Molecular Biology, pp. 314-321. AAAI Press. Menlo Park, CA.
36. Rost, B. and Sander, C. (1993) Prediction of protein secondary structure at better than 70% accuracy. J. Mol. Biol., 232, 584-599.
37. Russell, R.B., Copley, R.R. and Barton, G.J. (1996) Protein fold recognition by mapping predicted secondary structures. J. Mol. Biol., 259, 349-365.
38. Schneider, R. and Sander, C. (1991) Database of homology derived structures and the structural meaning of sequence alignment. Proteins: Struct. Funct. Genet., 9, 56-68.
39. Sheridan, R.P., Dixon, J.S. and Venkataraghavan, R. (1985) Generating plausible folds by secondary structure similarity. Int. J. Peptide Protein Res., 25, 132-143.
40. Somers, W., Stahl, M. and Seehra, J.S. (1997) 1.9 Å crystal structure of interleukin 6: implications for a novel mode of receptor dimerization and signaling. EMBO J., 16, 981-997.
41. Xu, G.Y. Hong, J., McDonagh, T., Sathl, M., Kay, L.E., Seehra, J. and Cumming, D.A. (1996) Complete 1H, 15N and 13C assignments. secondary structure, and topology of recombinant human interleukin-6. J. Biomol. NMR, 8, 123-135.