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J Mol Biol. 1998 Feb 6;275(5):895-916.

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

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Center for Advanced Research in Biotechnology, University of Maryland Biotechnology Institute, 9600, Gudelsky Drive, Rockville, MD 20850, USA.


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.

[Indexed for MEDLINE]

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