TMpred - Prediction of trans-membrane regions and orientation - ISREC (Swiss Institute for Experimental Cancer Research) Several great sites for online analysis of potential membrane spanning proteins are: ( Test sequence see Orientation of Proteins in Membranes for 268 unique a-helical membrane protein structures ) Also see: SCRATCH Protein Predictor (Institute for Genomics & Bioinformatics, University of California, Irvine, U.S.A.) For a metasite linked to a wide range of protein sequence analysis and structure predictions online programs, I recommend PredictProtein (ROSTLAB, Technische Universität München). MCSM-membrane - predicts the effects of mutations on transmembrane proteins. 3D structure generation) into a single prediction pipeline. Unlike most other tools or servers, PROTEUS2 bundles signal peptide identification, transmembrane helix prediction, transmembrane β-strand prediction, secondary structure prediction (for soluble proteins) and homology modeling (i.e. PROTEUS2 accepts either single sequences (for directed studies) or multiple sequences (for whole proteome annotation) and predicts the secondary and, if possible, tertiary structure of the query protein(s). PROTEUS2 - is a web server designed to support comprehensive protein structure prediction and structure-based annotation. From this one can study the secondary structure content of homologous proteins (a protein family) and highlight its structural patterns. The view 2D-alignment has been designed to visualise conserved secondary structure elements in a multiple sequence alignment (MSA). It provides two main functionalities: 2D-alignment and compare predictions. Thus it is important to develop seperate method for predicting secondary structure of peptides instead of using protein secondary structure prediction methods.ĢdSS (Biologie Computationnelle et Quantitative, Sorbonne Université, Paris, France) - is a web-server for visualising and comparing secondary structure predictions. Peptides may adopt diffrent secondary structure when integrated in proteins. Till date all the secondary structure prediction methods are optimized for proteins. 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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