Protein secondary structure: entropy, correlations and prediction.
BACKGROUND
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.


BACKGROUND
Both the data sets and analysis code are freely available from our Web site at http://compbio.berkeley.edu/
Crooks
Gavin E
GE
Department of Plant and Microbial Biology, University of California, 111 Koshland Hall No. 3102, Berkeley, CA 94720-3102, USA. gec@compbio.berkeley.edu
Brenner
Steven E
SE
D000465:Algorithms; D000595:Amino Acid Sequence; D003198:Computer Simulation; D019277:Entropy; D008390:Markov Chains; D008956:Models, Chemical; D008958:Models, Molecular; D015233:Models, Statistical; D008969:Molecular Sequence Data; D017433:Protein Structure, Secondary; D011506:Proteins / Q000032:analysis / Q000737:chemistry*; D016415:Sequence Alignment / Q000379:methods*; D020539:Sequence Analysis, Protein / Q000379:methods*; D017386:Sequence Homology, Amino Acid; D013223:Statistics as Topic
D011506:Proteins