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1: Bioinformatics. 2004 Jul 10;20(10):1603-11. Epub 2004 Feb 26.
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Protein secondary structure: entropy, correlations and prediction.

Crooks GE, Brenner SE.

Department of Plant and Microbial Biology, University of California, 111 Koshland Hall No. 3102, Berkeley, CA 94720-3102, USA. gec@compbio.berkeley.edu

MOTIVATION: Is protein secondary structure primarily determined by local interactions between residues closely spaced along the amino acid backbone or by non-local tertiary interactions? To answer this question, we measure the entropy densities of primary and secondary structure sequences, and the local inter-sequence mutual information density. RESULTS: We find that the important inter-sequence interactions are short ranged, that correlations between neighboring amino acids are essentially uninformative and that only one-fourth of the total information needed to determine the secondary structure is available from local inter-sequence correlations. These observations support the view that the majority of most proteins fold via a cooperative process where secondary and tertiary structure form concurrently. Moreover, existing single-sequence secondary structure prediction algorithms are almost optimal, and we should not expect a dramatic improvement in prediction accuracy. AVAILABILITY: Both the data sets and analysis code are freely available from our Web site at http://compbio.berkeley.edu/

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PMID: 14988117 [PubMed - indexed for MEDLINE]