Raghava, Scientist & Head Bioinformatics Center, Institute of Microbial Technology, India) - this Peptide Secondary Structure Prediction server that allows users to predict regular secondary structure in their peptides (e.g., H: Helix, E:Strand, C:Coil). They have also added important resources for the prediction of protein function. by adding predictions of non-regular secondary structure and intrinsically disordered regions, disulphide bridges and inter-residue contacts, and finally by also covering trans-membrane beta barrels structures. PredictProtein 2013 (Technical University of Berlin, Germany) - they have substantially expanded the breadth of structural annotations, e.g. RaptorX also assigns confidence scores to predicted structures.( Reference: Yang Y et al. RaptorX predicts protein secondary and tertiary structures, contact and distance map, solvent accessibility, disordered regions, functional annotation and binding sites. RaptorX - RaptorX excels at secondary, tertiary and contact prediction for protein sequences without close homologs in the Protein Data Bank (PDB). In addition to protein secondary structure, JPred also makes predictions of solvent accessibility and coiled-coil regions. JPred4 - is the latest version of the popular JPred protein secondary structure prediction server which provides predictions by the JNet algorithm, one of the most accurate methods for secondary structure prediction. See here for a more recent evaluation ( Reference: Yang Y et al. Running a secondary structure prediction on a newly-determined sequence just because everyone else does so, is to be deplored, and the fact that the results of such predictions are generally ignored is insufficient justification for doing and publishing them." Arthur Lesk, 1988. This is true even of the best methods now known, and much more so of the less successful methods commonly available in sequence analysis packages.
Precautionary Quote: " We should be quite remiss not to emphasize that despite the popularity of secondary structural prediction schemes, and the almost ritual performance of these calculations, the information available from this is of limited reliability. Online Analysis Tools - Protein Secondary Structure PROTEIN SECONDARY STRUCTURE
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