Simple hidden Markov models are proposed for predicting secondary structure of a protein from its amino acid sequence. Since the length of protein conformation segments varies in a narrow range, we ignore the duration effect of length distribution, and focus on inclusion of short range correlations of residues and of conformation states in the models. Conformation-independent and -dependent ami...

All existing algorithms for predicting the content of protein secondary structure elements have been based on the conventional amino-acid-composition, where no sequence coupling effects are taken into account. In this article, an algorithm was developed for predicting the content of protein secondary structure elements that was based on a new amino-acid-composition, in which the sequence coupli...

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-sequenc...

http://www.hgmp.mrc.ac.uk/Registered/Option/stride.html Protein Secondary Structure Assignment and Prediction Defining SS features Dihedral angles, alpha helix, beta stand (Hydrogen bonds) Assigned manually by crystallographers or Automatic DSSP (Kabsch & Sander,1983) STRIDE (Frishman & Argos, 1995) Continuum PCE: Protein Continuum Electrostatics (Andersen et al.) http://bioserv.rpbs.jussieu.fr...

Information about the secondary and tertiary structure of a protein sequence can greatly assist biologists in the generation and testing of hypotheses, as well as design of experiments. The PROTINFO server enables users to submit a protein sequence and request a prediction of the three-dimensional (tertiary) structure based on comparative modeling, fold generation and de novo methods developed ...