Protein Analysis (Online Services)

Protein Analysis Sites:

Entelechon Backtranslation tool Entelechon Backtranslation tool: Online backtranslation tool for translating a protein sequence into a DNA sequence. The codon usage can be downloaded from a database and adjusted manually for each amino acid, if required. Java applet. (Protein Analysis) http://www.entelechon.com/eng/backtranslation.html Jpred Jpred: Secondary protein structure prediction from amino acid sequence; based on a consensus from several methods including DSC, PHD, NNSSP, PREDATOR, ZPRED, and MULPRED. (Protein Analysis) http://www.compbio.dundee.ac.uk/~www-jpred/ ProtFun ProtFun: Ab initio predictions of protein function from protein sequence. The method works by integrating various predicted post-translational and localizational aspects of the proteins submitted. (Protein Analysis) http://www.cbs.dtu.dk/services/ProtFun/ Quaternary Structure Prediction Quaternary Structure Prediction: An experimental bioinformatics server. Classifies protein sequences as homodimers or non-homodimers. Applications: metabolic reconstruction, protein structure and function assignment, and drug-design. (Protein Analysis) http://mericity.com/ Betapred Betapred: Prediction of beta turns and their types using statistical algorithms. 5 different methods including Chou-Fasman, Thornton's PRs, Gorbturn, and a consensus of all methods. (Protein Analysis) http://imtech.res.in/raghava/betatpred Protein Structure Prediction Server (PSIPRED) Protein Structure Prediction Server (PSIPRED): 3D protein structure prediction from amino acid sequence. Includes MEMSAT for transmembrane topology prediction, GenTHREADER and mGenTHREADER for fold recognition. (Protein Analysis) http://bioinf.cs.ucl.ac.uk/psipred/ Munich Information Center for Protein Sequences (MIPS) Munich Information Center for Protein Sequences (MIPS): Bioinformatics research group offering organism specific information (Yeast, Cress) as well as search tools for public databases. (Protein Analysis) http://mips.gsf.de/ InterPro - The Integrated Resource of Protein Domains and Functional Sites. InterPro - The Integrated Resource of Protein Domains and Functional Sites.: A database built from Pfam, PRINTS and PROSITE. (Protein Analysis) http://www.ebi.ac.uk/interpro/ PDB Ligand Environment PDB Ligand Environment: Ligand search engine to EBI Macromolecule Structure Database. Provides PDB ID codes with further visualization and statistics charts. (Protein Analysis) http://www.ebi.ac.uk/msd-srv/msdsite EMBL Bioinformatic Harvester EMBL Bioinformatic Harvester: Collection of human (swall) proteins, crossreferences to major prediction servers. Supported predictions from: smart, string, blast, swall, mapview, sosui, ipsort and ncbi conserved domains. (Protein Analysis) http://harvester.embl.de JAligner JAligner: Java Applet for an implementation of Smith-Waterman algorithm for pairwise biological sequence alignment using dynamic programming (extended to support affine gap penalties) download or launch from site. (Protein Analysis) http://foobox.com/~ahmed/jaligner Swiss-Model Swiss-Model: Automated comparative protein modelling server to make protein modelling accessible to biochemists and molecular biologists worldwide - from GlaxoWellcome Experimental Research, Geneva, Switzerland. (Protein Analysis) http://www.expasy.ch/swissmod/SWISS-MODEL.html Protonet Protonet: Provides automatic hierarchical classification of proteins sequences. (Protein Analysis) http://www.protonet.cs.huji.ac.il 3D-JIGSAW 3D-JIGSAW: Automated comparative (homology) protein modelling, including an interactive mode which highlights known domains and allows users to select and align templates. (Protein Analysis) http://www.bmm.icnet.uk/~3djigsaw/ Proteomics Analysis: Z3 and LabOnWeb's Z3OnWeb Proteomics Analysis: Z3 and LabOnWeb's Z3OnWeb: Proteomic analysis for analyzing 2D-Gel images. Use Compugen's Z3 or Z3OnWeb utitlities for automatic spot detection and registration (=alignment) of protein gel images to match the spots. (Protein Analysis) http://www.2dgels.com SWISS-PROT + TrEMBL SWISS-PROT + TrEMBL: The SWISS-PROT database contains high-quality annotation, is non-redundant and cross-referenced to many other databases. SWISS-PROT is accompanied by TrEMBL, a computer-annotated supplement, which contains the translations of all coding sequences (CDS) pr (Protein Analysis) http://www.ebi.ac.uk/swissprot/ The Protein Information Resource The Protein Information Resource: In collaboration with the Munich Information Center for Protein Sequences (MIPS) and the Japanese International Protein Sequence Database (JIPID) maintains the PIR-International Protein Sequence Database --- a comprehensive, annotated, and non-redundant (Protein Analysis) http://pir.georgetown.edu Molecular Biology Tools Online Molecular Biology Tools Online: Includes WebOligoMelt (Annealing temperature of oligonucleotides), Virtual Ribosome (translate nucleotide sequences into peptides), and SeqScanGraph (graph melting temperature along nucleotide chain). (Protein Analysis) http://mbt.biobitfield.com/ Combinatorial Extension of Polypeptides Combinatorial Extension of Polypeptides: Method for finding 3-D similarities in protein structures from the UCSD Supercomputer Center. (Protein Analysis) http://cl.sdsc.edu/ce.html Swiss-Pdb Viewer Swiss-Pdb Viewer: User-friendly interface allowing analysis of several proteins at once, including superimposition to deduce structural alignments, and compare active sites. From GlaxoWellcome Experimental Research, Geneva, Switzerland. (Protein Analysis) http://www.expasy.ch/spdbv/ PredictProtein Server PredictProtein Server: Most widely used server for analysing protein sequences, searching protein databases, and predicting protein structure - from Columbia Univ. (Protein Analysis) http://cubic.bioc.columbia.edu/predictprotein/ Proteomics Tools Proteomics Tools: Online software for protein analysis from the Swiss Institute of Bioinformatics (SIB). (Protein Analysis) http://www.expasy.ch/tools/ 3D-PSSM Fold Recognition 3D-PSSM Fold Recognition: Combines sequence and structural information for predicting the structure and/or function of your protein sequence, and can detect remote homologies beyond PSI-Blast. (Protein Analysis) http://www.sbg.bio.ic.ac.uk/~3dpssm/