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PubMed · 9480776

An all-atom distance-dependent conditional probability discriminatory function for protein structure prediction.

R Samudrala·J Moult
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Abstract

We present a formalism to compute the probability of an amino acid sequence conformation being native-like, given a set of pairwise atom-atom distances. The formalism is used to derive three discriminatory functions with different types of representations for the atom-atom contacts observed in a database of protein structures. These functions include two virtual atom representations and one all-heavy atom representation. When applied to six different decoy sets containing a range of correct and incorrect conformations of amino acid sequences, the all-atom distance-dependent discriminatory function is able to identify correct from incorrect more often than the discriminatory functions using approximate representations. We illustrate the importance of using a detailed atomic description for obtaining the most accurate discrimination, and the necessity for testing discriminatory functions against a wide variety of decoys. The discriminatory function is also shown to be capable of capturing the fine details of atom-atom preferences. These results suggest that the all-atom distance-dependent discriminatory function will be useful for protein structure prediction and model refinement.

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Models, TheoreticalProbabilityProtein ConformationStatic ElectricityJournal ArticleResearch Support, Non-U.S. Gov'tResearch Support, U.S. Gov't, P.H.S.

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R Samudrala, J Moult. 1998-02-06. An all-atom distance-dependent conditional probability discriminatory function for protein structure prediction.. https://doi.org/10.1006/jmbi.1997.1479

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