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• 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.
• BioInfoBank Meta Server - Offers a gateway to well-benchmarked protein structure and function prediction methods. Structural models collected from the predictions servers are assessed using the powerful 3D-jury consensus approach.
• COLORADO3D - Service to aid visualisation of potential errors in protein structures. Free for academic users.
• Combinatorial Extension of Polypeptides - Method for finding 3-D similarities in protein structures from the UCSD Supercomputer Center.
• ConSurf - Identifies functionally important regions on the surface of a protein or domain, of known three-dimensional (3D) structure using the phylogenetic relations between close sequence homologues.
• Dali server - The Dali server is a network service for comparing protein structures in 3D.
• DisEMBL - Computational tool for sequence based prediction of intrinsic protein disorder and unstructured regions within a protein.
• 3D-JIGSAW - Automated comparative (homology) protein modelling, including an interactive mode which highlights known domains and allows users to select and align templates.
• 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.
• ELM - Functional Sites in Proteins - Predicts functional sites (linear motifs) in proteins, such as post-translational modification sites, ligand motifs, and targeting signals. Context-based rules and logical filters are applied to improve predictions.
• 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.
• 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.
• ESyPred3D - ESyPred3D is an automated homology modeling program getting benefit of the increased alignment performances of a new alignment strategy using neural networks. The final three dimensional structure is built using the modeling package MODELLER.
• iMolTalk - Provides protein structure information such as structural alignment, residue contact, protein-protein interfaces, contact maps and general information extraction.
• InterPro - The Integrated Resource of Protein Domains and Functional Sites. - A database built from Pfam, PRINTS and PROSITE.
• Isoelectric Point Estimator - Calculated using the FASTA amino acid sequence and pKa values for. Allows consideration of post-translational modifications.
• JAligner - Open source Java implementation of the dynamic programming algorithm Smith-Waterman for biological local pairwise sequence alignment.
• Jpred - Secondary protein structure prediction from amino acid sequence; based on a consensus from several methods including DSC, PHD, NNSSP, PREDATOR, ZPRED, and MULPRED.
• Melanie II 2-D Analysis Software - Powerful, state-of-the-art, 2-D analysis software package with user-friendly interface from the Swiss Institute of Bioinformatics.
• MODBASE - A database of annotated comparative protein structure models. The database includes fold assignments and alignments as well as information about putative ligand binding sites, SNP annotation, and protein-protein interactions.
• 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).
• Molecules To Go - Search engine for visualizing 3-D biomolecular models. From the Center for Molecular Modeling, NIH, Maryland.
• MSDmotif - Service for protein sequence motifs detection. Search based on the small 3D motifs defined by J.Milner-White.
• MultiProt - Service for detecting the multiple structural alignments of proteins. Uses the common geometrical cores between the input molecules. Does not require that all the input molecules participate in the alignment.
• Munich Information Center for Protein Sequences (MIPS) - Bioinformatics research group offering organism specific information (Yeast, Cress) as well as search tools for public databases.
• NUMODs Motifs Finder - Finds Nuclease-Associated Modular DNA-binding Domains (NUMODs) in protein sequences
• PDB Ligand Environment - Ligand search engine to EBI Macromolecule Structure Database. Provides PDB ID codes with further visualization and statistics charts.
• PFP: Automated Function Prediction Server - Accepts a single query protein sequence and returns the most probable Gene Ontology functional annotations in each of the three ontologies.
• Phyre- Protein Homology/analogY Recognition Engine - Phyre is a free for academics service for predicting the 3-dimensional structure of a protein amino acid sequence.
• PredictProtein Server - Most widely used server for analysing protein sequences, searching protein databases, and predicting protein structure - from Columbia Univ.
• The ProCKSI Server: Protein Comparison, Knowledge, Similarity and Information - ProCKSI is a decision support system for protein structure comparison. It provides tools for visualising, analysing, clustering and comparing results.
• 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. An annotated, and non-redundant set of protein sequence databases in which entries are classified into family groups and alignments of each group are available.
• 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.
• Proteomics Tools - Online software for protein analysis from the Swiss Institute of Bioinformatics (SIB).
• 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.
• Protonet - Provides automatic hierarchical classification of proteins sequences.
• 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.
• SSM - Provides interactive service for matching protein structures in 3D and looking for structural homologues in PDB and SCOP databases, as well as in user-uploaded sets of structures.
• Swiss-Model - Automated comparative protein modelling server to make protein modelling accessible to biochemists and molecular biologists worldwide - from GlaxoWellcome Experimental Research, Geneva, Switzerland.
• 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.
• 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) present in the EMBL Nucleotide Sequence Database, which are not yet integrated into SWISS-PROT.
• TopMatch: Protein Structure Comparison - Public web service for the alignment and superposition of protein structures and the instant visualization of structural similarities.
• TRANSFAC-The Transcription Factor Database - A compilation of transcriptional regulatory protein factors and their cognate gene promoter elements along with DNA sequence search and analysis programs - from GBF, Braunschweig, Germany.
• UniProt - UniProt (Universal Protein Resource) is a catalog of information on proteins. It is a central repository of protein sequence and function created by joining the information contained in Swiss-Prot, TrEMBL, and PIR.
• Wurst - A protein threading server using sequence profiles combined with a protein sequence to structure compatibility function based on Bayesian statistics.

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