Abstract
THE prediction of protein tertiary structure from sequence using molecular energy calculations has not yet been successful; an alternative strategy of recognizing known motifs1 or folds2–4 in sequences looks more promising. We present here a new approach to fold recognition, whereby sequences are fitted directly onto the backbone coordinates of known protein structures. Our method for protein fold recognition involves automatic modelling of protein structures using a given sequence, and is based on the frameworks of known protein folds. The plausibility of each model, and hence the degree of compatibility between the sequence and the proposed structure, is evaluated by means of a set of empirical potentials derived from proteins of known structure. The novel aspect of our approach is that the matching of sequences to backbone coordinates is performed in full three-dimensional space, incorporating specific pair interactions explicitly.
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References
Taylor, W. R. & Thornton, J. M. J. molec. Biol. 173, 487–514 (1984).
Overington, J., Johnson, M. S., Šali, A. & Blundell, T. L. Proc. R. Soc. B241, 132–145 (1990).
Finkelstein, A. V. & Reva, B. A. Nature 351, 497–499 (1991).
Bowie, J. U., Lüthy, R. & Eisenberg, D. Science 253, 164–170 (1991).
Bernstein, F. C. et al. J. molec. Biol. 112, 535–542 (1977).
Dayhoff, M. O., Schwartz, R. M. & Orcutt, B. C. in Atlas of Protein Sequence and Structure Vol. 5 suppl. 3 345–352 (Natn. Biomed. Res. Fnd, Washington DC, 1978).
Thornton, J. M., Flores, T. P., Jones, D. T. & Swindells, M. B. Nature 354, 105–106 (1991).
Taylor, W. R. & Orengo, C. A. J. molec. Biol. 208, 1–22 (1989).
Orengo, C. A. & Taylor, W. R. J. theor. Biol. 147, 517–551 (1990).
Novotny, J., Bruccoleri, R. E. & Karplus, M. J. molec. Biol. 177, 787–818 (1984).
Brooks, B. et al. J. comp. Chem. 4, 187–217 (1983).
Hendlich, M. et al. J. molec. Biol. 216, 167–180 (1990).
Eisenberg, D. & McLachlan, A. D. Nature 319, 199–203 (1986).
Sippl, M. J. J. molec. Biol. 213, 859–883 (1990).
Schirmer, T., Bode, W., Huber, R., Sidler, W. & Zuber, H. J. molec. Biol. 184, 257–277 (1985).
Bashford, D., Chothia, C. & Lesk, A. M. J. molec. Biol. 196, 199–216 (1987).
Pastore, A. & Lesk, A. M. Proteins 8, 133–155 (1990).
Taylor, W. R. Prot. Engng 4, 853–870 (1991).
Kabsch, W. & Sander C. Biopolymers 22, 2577–2637 (1983).
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Jones, D., Taylort, W. & Thornton, J. A new approach to protein fold recognition. Nature 358, 86–89 (1992). https://doi.org/10.1038/358086a0
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DOI: https://doi.org/10.1038/358086a0
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