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...

Understanding protein biological function is a key issue in modern biology, which is largely determined by its 3D shape. Protein 3D shape, in its turn, is functionally implied by its amino acid sequence. Since the direct inspection of such 3D structures is rather expensive and time consuming, a number of software techniques have been developed in the last few years that predict a spatial model,...

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...

We present a novel method for predicting the secondary structure of a protein from its amino acid sequence. Most existing methods predict each position in turn based on a local window of residues, sliding this window along the length of the sequence. In contrast, we develop a probabilistic model of protein sequence/structure relationships in terms of structural segments, and formulate secondary...

Princeton University 29.

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 ...

Predicting protein structure from amino acid sequence is one of the most important unsolved problems of molecular biology and biophysics.Not only would a successful prediction algorithm be a tremendous advance in the understanding of the biochemical mechanisms of proteins , but , since such an algorithm could conceivably be used to design proteins to carry out specific functions.Prediction of t...

Proteins contain a large fraction of regular, repeating conformations, called secondary structure. A simple, generic definition of secondary structure is presented which consists of measuring local correlations along the protein chain. Using this definition and a simple model for proteins, the forces driving the formation of secondary structure are explored. The relative role of energy and entr...

In order to compare orthogonal encoding, five bye encoding, codon encoding (two) and profile encoding to find out their virtues and shortcomings, we carefully studied them with artificial neural network. Results indicate that profile encoding that preserves the redundant evolutionary information gets higher predictive performance. The experimental results show that combining profile encoding an...