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Vol 20 no 10 2004 pages 1603 1611 doi 10 1093 bioinformatics bth132 BIOINFORMATICS Protein secondary structure entropy correlations and prediction Gavin E Crooks and Steven E Brenner Department of Plant and Microbial Biology University of California 111 Koshland Hall No 3102 Berkeley CA 94720 3102 USA Received on November 4 2003 revised and accepted on November 26 2003 Advance Access publication February 26 2004 ABSTRACT 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 Contact gec compbio berkeley edu INTRODUCTION The secondary structure of a protein is a summary of the general conformation and hydrogen bonding pattern of the amino acid backbone Frishman and Argos 1995 This structure is frequently simplified to a sequence one element per residue of helixes H extended strands E and unstructured loops L It has long been recognized that each residue s secondary structure is appreciably correlated with the local amino acid sequence Szent Gyorgyi

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