Abstract
Proteins frequently adopt similar three-dimensional folds even if there is no detectable homology on the sequence level. Therefore, it is likely that a substantial fraction of known sequences will have native folds which resemble some known structure. The task of fold recognition is to identify such coincidences, thereby predicting the unknown folds of known amino acid sequences. We present the principles of a fold recognition technique based on mean force potentials and apply the procedure in two case studies, demonstrating that the method is able to recognize native-like sequence structure pairs in cases where no significant sequence homology is detectable.
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References
J. Novotny, R. Bruccoleri and M. Karplus: J. Mol. Biol. 177 ,787 (1984)
M. J. Sippl: Proteins 7, 355 (1993a).
S. J. Wodak and M. J. Rooman: Curr. Opp. Struct. Biol. 3, 247 (1993)
J. U. Bowie and D. Eisenberg: Curr. Opp. Struct. Biol. 3, 437 (1993)
M. J. Sippl: J. Comput. Aided. Mol. Design 473 ,(1993b)
J. S. Fetrow and S. H. Bryant: Biotechnology 11, 479 (1993)
R. Luthy, J. U. Bowie and D. Eisenberg: Nature 356, 83 (1992).
K. E. Drexier: Proc. Natl. Acad. Sci. USA 78, 5275 (1981).
J. W.Ponder and F. M. Richards: J. Mol. Biol. 193, 775 (1987).
J. U. Bowie, R. Liithy and D. Eisenberg: Science 253, 164 (1991).
M. J. Sippl, H. Flockner and S. Weitckus: ‘In search of protein folds’, in K. Merz and S. LeGrand, Eds. The Protein Folding Problem and Tertiary Structure Prediction ,Birkhäuser, Boston, in press (1994a).
M. J. Sippl: J. Mol. Biol. 213, 859 (1990).
M. Hendlich, P. Lackner, S. Weitckus, H. Flöckner, R. Froschauer, K. Gottsbacher, G. Casari, and M. J. Sippl: J. Mol. Biol. 216, 167 (1990).
M. J. Sippl, M. Jaritz, M. Hendlich, M. Ortner and P. Lackner: ‘Applications of knowledge based mean fields in the determination of protein structures’, in S. Doniach, Eds., Statistical Mechanics, Protein Structure and Protein-substrate Interactions ,Plenum Publishers, in press (1994b).
M. J. Sippl and M. Jaritz: ‘Predictive power of mean force pair potentials’, in H. Bohr and S. Brunak, Eds., Protein Structure by Distance Analysis ,IOS Press, Amsterdam, pp. 113–134 (1994).
D. T. Jones, W. R. Taylor, and J. M. Thornton: Nature 358, 86 (1992).
S. B. Needleman and C. D. Wunsch: J. Mol. Biol. 48, 443 (1970).
J. Kim and D. C. Rees: Science 257, 1677 (1992a).
I. Schlichting, S. C. Almo, G. Rapp, K. Wilson, K. Petratos, A. Lentfer, A. Wittinghofer, W. Kabsch, E .F. Pai, G. A. Petsko, and R. S. Goody: Nature 345, 309 (1990).
H. R. Bourne, D. A. Sanders, and F. McCormick: Nature 349, 117 (1991).
J. Ahnn, P. E. March, H. E. Takiff, and M. Inouye: Proc. Natl. Acad. Sci. USA 83, 8849 ((1986).
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Sippl, M.J., Weitckus, S., Flöckner, H. (1995). Fold Recognition. In: Pullman, A., Jortner, J., Pullman, B. (eds) Modelling of Biomolecular Structures and Mechanisms. The Jerusalem Symposia on Quantum Chemistry and Biochemistry, vol 27. Springer, Dordrecht. https://doi.org/10.1007/978-94-011-0497-5_10
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DOI: https://doi.org/10.1007/978-94-011-0497-5_10
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