Abstract
In protein-structure prediction, simplified energy functions are necessarily used to allow fast sorting over many conformations. As a rule, these functions are derived from residue-residue approximation, which attributes all atomic interactions between residues to a single point within each residue. Physically, the simplified energies should result from averaging of the atomic interactions over various positions and conformations of the interacting amino acid residues, as well as the surrounding solvent molecules. Unfortunately, direct calculation of such mean-force potentials is not possible today both because of methodological difficulties and the lack of reliable atom-based energy functions.
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References
Sippl, M. (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, 859–883.
Vajda, S., Sippl, M., and Novotny, J. (1997) Empirical potentials and functions for protein folding and binding. Curr. Opin. Struct. Biol. 7(2), 222–228.
Thomas, P. D. and Dill, K. A. (1996) Statistical potentials extracted from protein structures: how accurate are they? J. Mol. Biol. 257, 457–469.
Godzik, A., Kolinski, A., and Skolnick, J. (1995) Are proteins ideal mixtures of amino acids? Analysis of energy parameter sets. Prot. Sci. 4, 2107–2117.
Jernigan, R. and Bahar, I. (1996) Structure-derived potentials and protein simulations. Curr. Opin. Struct. Biol. 6, 195–209.
Rooman, J. and Wodak, S. (1995) Are database-derived potentials valid for scoring both forward and inverted protein folding? Protein Eng. 8, 849–858.
Skolnick, J., Jaroszewski, L., Kolinski, A., and Godzik, A. (1997) Derivation and testing of pair potentials for protein folding. When is the quasichemical approximation correct? Prot. Sci. 6(3), 676–688.
Kocher, J. P., Rooman M. J., and Wodak S. J. (1994) Factors influencing the ability of knowledge-based potentials to identify native sequence-structure matches. J. Mol. Biol. 235(5), 1598–1613.
Pohl, F. M. (1971) Empirical protein energy maps. Nat. New Biol. 234, 277–279.
Finkelstein, A., Badretdinov, A., and Gutin, A. (1995) Why do protein architectures have Boltzmann-like statistics? Proteins 23, 142–150.
Reva, B. A., Finkelstein, A. V., Sanner, M. F., and Olson, A. J. (1997) Accurate mean-force pairwise-residue potentials for discrimination of protein folds, in Proceedings of Pacific Symposium on Biomolecular Computations, 373–384.
Reva, B. A., Finkelstein, A. V., Sanner, M. F., and Olson, A. J. (1997) Residueresidue mean-force potentials for protein structure recognition. Protein Eng. 10(5), 865–876.
Hobohm, U., Scharf, M., Schneider, R., and Sander, C. (1992) Selection of representative protein data sets. Prot. Sci. 1, 409–417.
Smith, T. and Waterman, M. (1981) Identification of common molecular subsequences. J. Mol. Biol. 147, 195–197.
Murzin, A., Brenner, S., 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.
Ben-Naim, A. (1997) Statistical potentials extracted from protein structures: are these meaningful potentials? J. Chem. Phys. 107(9), 3698–3706.
Hendlich, M., Lackner, P., Weitckus, S., Floeckner, H., Froschauer, R., Gottsbacher, K., Casari, G., and Sippl, M. (1990) Identification of native protein folds amongst a large number of incorrect models. The calculation of low energy conformations from potentials of mean force. J. Mol. Biol. 216, 167–180.
Shakhnovich, E. I. and Gutin, A. M. (1989) Formation of unique structure in polypeptide chain. Theoretical investigation with the aid of a replica approach. Biophys. Chem. 34, 187–199.
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Reva, B.A., Finkelstein, A.V., Skolnick, J. (2000). Derivation and Testing Residue-Residue Mean-Force Potentials for Use in Protein Structure Prediction. In: Webster, D.M. (eds) Protein Structure Prediction. Methods in Molecular Biology™, vol 143. Humana Press. https://doi.org/10.1385/1-59259-368-2:155
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DOI: https://doi.org/10.1385/1-59259-368-2:155
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