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An iterative method for extracting energy-like quantities from protein structures.

P D Thomas·K A Dill
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Abstract

We present a method (ENERGI) for extracting energy-like quantities from a data base of protein structures. In this paper, we use the method to generate pairwise additive amino acid "energy" scores. These scores are obtained by iteration until they correctly discriminate a set of known protein folds from decoy conformations. The method succeeds in lattice model tests and in the gapless threading problem as defined by Maiorov and Crippen [Maiorov, V. N. & Crippen, G. M. (1992) J. Mol. Biol. 227, 876-888]. A more challenging test of threading a larger set of test proteins derived from the representative set of Hobohm and Sander [Hobohm, U. & Sander, C. (1994) Protein Sci. 3, 522-524] is used as a "workbench" for exploring how the ENERGI scores depend on their parameter sets.

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Amino Acid SequenceAmino AcidsBinding SitesBiophysicsModels, ChemicalProtein ConformationProtein FoldingProteinsJournal ArticleResearch Support, Non-U.S. Gov'tResearch Support, U.S. Gov't, P.H.S.

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P D Thomas, K A Dill. 1996-10-15. An iterative method for extracting energy-like quantities from protein structures.. https://doi.org/10.1073/pnas.93.21.11628

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