Prediction of transmembrane spans and secondary structure from the protein sequence is generally the first step in the structural characterization of (membrane) proteins. Preference of a stretch of amino acids in a protein to form secondary structure and being placed in the membrane are correlated. Nevertheless, current methods predict either secondary structure or individual transmembrane stat...

Prediction of protein secondary structures is one of the oldest problems in Bioinformatics. Although several different methods have been proposed to tackle this problem, none of these methods are perfect. Recently, it is proposed that addition of other structural information like accessible surface area of residues or prior information about protein structural class can significantly improve th...

Prediction of protein secondary structures is an important problem in bioinformatics and has many applications. Successful secondary structure predictions provide a starting point for direct tertiary structure modelling, and also can significantly improve sequence analysis and sequence-structure threading for aiding in structure and function determination. Now many secondary structure predictio...

Here we propose an approach to include global structural information in the secondary structure prediction procedure based on hidden Markov models (HMMs) of protein folds. We first identify the correct fold or 'topology' of a protein by means of the HMMs of topology families of proteins. Then the most likely structural model for that protein is used to modify the sequence of secondary structure...

Protein structure prediction has always been an important research area in biochemistry. In particular, the prediction of protein secondary structure has been a well-studied research topic. The experimental methods currently used to determine protein structure are accurate, yet costly both in terms of equipment and time. Despite the recent breakthrough of combining multiple sequence alignment i...

The expected best residue-by-residue accuracies for secondary structure prediction from multiple protein sequence alignment have been determined by an analysis of known protein structural families. The results show substantial variation is possible among homologous protein structures, and that 100% agreement is unlikely between a consensus prediction and one member of a protein structural famil...