Protein fold recognition by sequence threading: Tools and assessment techniques

FASEB Journal

Volumn 10, Issue 1, 1996, Pages 171-178

  Miller, R T ^a   Jones, D T ^a,b   Thornton, J M ^a  

^a UNIVERSITY COLLEGE LONDON   (United Kingdom)

^b NATIONAL INSTITUTE FOR MEDICAL RESEARCH   (United Kingdom)

Author keywords

protein folding; protein structure prediction; protein threading

Indexed keywords

ARTICLE; COMPUTER ANALYSIS; COMPUTER PROGRAM; MOLECULAR RECOGNITION; PREDICTION; PRIORITY JOURNAL; PROTEIN FOLDING;

EID: 0030052366     PISSN: 08926638     EISSN: None     Source Type: Journal    
DOI: 10.1096/fasebj.10.1.8566539     Document Type: Article

References (32)

1. Eisenhaber, F., Persson, B., and Argos, P. (1995) Protein Structure Prediction: Recognition of primary, secondary, and tertiary structural features from aminu acid sequence. Crit. Rev. Biochem. Mol. Biol. 30, 1-94
2. Matsuo, Y., and Nishikawa, K. (1994) Protein structural similarities predicted by a sequence-structure compatibility method. Protein Sci. 3, 2055-2063
3. Bryant, S. H., and Lawrence, C. E. (1993) An empirical energy function for threading protein sequence through the folding motif. Proteins: Struct. Funct. Genet. 16, 92-112
4. Godzik, A., and Skolnik, J. (1992) Sequence-structure matching in globular proteins: Application to supersecondary and tertiary structure determination. Proc. Natl. Acad. Sci. USA 89, 12098-12102
5. Jones, D. T., Taylor, W. R., and Thornton, J. M. (1992) A new approach to protein fold recognition. Nature (London) 358, 86-89
6. 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
7. Jones, D. T., Miller, R. T., and Thornton, J. M. (199?) Successful protein fold recognition by optimal sequence threading validated by rigorous blind testing. Protein Sci. In press
8. BSM home WWW page. http://www.biochem.ucl.ac.uk/bsm/biocomp/in-dex.html
9. BSM anonymous ftp site, ftp://ftp.biochem.ucl.ac.uk/pub
10. 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, 859-853
11. CATH WWW page. http://www.biochem.ucl.ac.uk/bsm/cath/CATHin-tro.html
12. Jones, D. T., and Thornton, J. M. (1993) Protein fold recognition. J. Computer-Aided Mol. Design 7, 439-456
13. Taylor, W. R., and Orengo, C. A. (1989) Protein structure alignment. J. Mol. Biol. 208, 1-22
14. Lathrop, R. (1994) The protein threading problem with sequence amino acid interaction preferences is NP-complete. Protein Eng. 7, 1059-1068
15. Ousterhout, J. K. (1994) Tcl and the Tk Toolkit, 458 pp., Addison-Wesley Publishing Company, Reading, Massachusetts
16. Bernstein, F. C., Koetzle, T. F., Williams, G. J. B., Meyer, E. F., Jr., Brice, M. D., Rodgers, J. R., Kennard, O., Shimanouchi, T., and Tasumi, M. (1977) The Protein Data Bank: A computer-based arehival file for maeromolecular structures. J. Mol. Biol. 112, 535-542
17. Abola, E. E., Bernstein, F. C., Bryant, S. H., Koetzle, T. F., and Weng, J. (1987) Protein Data Bank In Crystallographic Databases - Information Content, Software Systems, Scientific Applications (Allen, F. H., Bergerhoff, G., and Sievers, R., eds) pp. 107-132, Data Commission of the International Union of Crystallography, Bonn, Germany
18. Chou, P. Y., and Fasman, G. D. (1974) Conformational parameters foramino acids in helical, beta-sheet and random coil regions calculated from proteins. Biochemistry 13, 211-222
19. Kyte, J., and Doolittle, R. F. (1982) A simple method for displaying the hydropathic character of a protein. J. Mol. Biol. 157, 105-132
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. Sayle, R. A., RasMol molecular viewing program, available by anonymous ftp from ftp.dcs.ed.ac.uk:/pub/rasmol
22. Sowdhamini, R., and Blundell, T. L. (1995) An automatic method involving cluster analysis of secondary structures for the identification of domains in proteins. Protein Sci. 4, 506-520
23. Kikuchi, T., Nemethy, G., and Scheraga, H. (1988) Prediction of the location of structural domains in globular proteins. J. Protein Chem. 7, 427-471
24. Zehfus, M. H., and Rose, G. D. (1986) Compact units in proteins. Biochemistry 25, 5759-5765
25. Wodak, S., and Janin, J. (1981) Location of structural domains in proteins. Biochemistry 20, 6544-6552
26. Levitt, M., and Chothia, C. (1976) Structural patterns in globular proteins. Nature (London) 261, 552-558
27. Miller, R. T., Douthart, R. J., and Dunker, A. K. (1994) Development and application of a three-dimensional description of amino acid environments in protein. In Advances in Molecular Bioinformatics, pp. 9-30, IOS Press, Amsterdam, Netherlands
28. Rost, B., Sander, C., and Schneider, R. (1994) PHD - a mail server for protein secondary structure prediction. CABIOS 10, 53-60
29. Benner, S. A. (1992) Predicting de novo the folded structure of proteins. Curr. Opin. Struct. Biol. 2, 402-412
30. Benner, S. A., Cohen, M. A., and Gonnet, G. H. (1993) Empirical and structural models for insertions and deletions in the evolution of proteins. J. Mol. Biol. 229, 1065-1082
31. Bryant, S., and Altschul, S. (1995) Statistics of sequence-structure threading. Curr. Opin. Struct. Biol. 5, 236-244
32. Jurnak, F., Yoder, M. D., Pickersgill, R., and Jenkins, J. (1995) Parallel β-domains: a new fold in protein structures. Curr. Opin. Struct. Biol. 5, 802-806