Protein secondary structure: entropy, correlations and prediction. Export

@article{citeulike:615468, 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/}, address = {Department of Plant and Microbial Biology, University of California, 111 Koshland Hall No. 3102, Berkeley, CA 94720-3102, USA. gec@compbio.berkeley.edu}, author = {Crooks, G. E. and Brenner, S. E.}, citeulike-article-id = {615468}, citeulike-linkout-0 = {http://view.ncbi.nlm.nih.gov/pubmed/14988117}, citeulike-linkout-1 = {http://www.hubmed.org/display.cgi?uids=14988117}, day = {10}, issn = {1367-4803}, journal = {Bioinformatics}, keywords = {information, protein}, month = {July}, number = {10}, pages = {1603--1611}, posted-at = {2008-11-24 15:04:36}, priority = {2}, title = {Protein secondary structure: entropy, correlations and prediction.}, url = {http://view.ncbi.nlm.nih.gov/pubmed/14988117}, volume = {20}, year = {2004} }

TY - JOUR ID - citeulike:615468 L3 - citeulike-article-id:615468 N2 - 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/ IS - 10 JF - Bioinformatics SN - 1367-4803 AD - Department of Plant and Microbial Biology, University of California, 111 Koshland Hall No. 3102, Berkeley, CA 94720-3102, USA. gec@compbio.berkeley.edu EP - 1611 TI - Protein secondary structure: entropy, correlations and prediction. VL - 20 SP - 1603 KW - information KW - protein AU - Crooks, GE AU - Brenner, SE PY - 2004/07/10/ UR - http://view.ncbi.nlm.nih.gov/pubmed/14988117 ER -