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» 3D-JIGSAW 
Automated comparative (homology) protein modelling, including an interactive mode which highlights known domains and allows users to select and align templates.
http://www.bmm.icnet.uk/~3djigsaw/
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» 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.
http://www.sbg.bio.ic.ac.uk/~3dpssm/
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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.
http://imtech.res.in/raghava/betatpred
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» COLORADO3D
Service to aid visualisation of potential errors in protein structures. Free for academic users.
http://asia.genesilico.pl/colorado3d/
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» 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.
http://consurf.tau.ac.il/overview.html
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» Dali server
The Dali server is a network service for comparing protein structures in 3D.
http://www.ebi.ac.uk/dali/
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» DisEMBL
Computational tool for sequence based prediction of intrinsic protein disorder and unstructured regions within a protein.
http://dis.embl.de
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» 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.
http://elm.eu.org
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» 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.
http://harvester.embl.de
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» 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.
http://www.fundp.ac.be/urbm/bioinfo/esypred/
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» 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.
http://www.entelechon.com/bioinformatics/backtranslation.php
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» Isoelectric Point Estimator
Calculated using the FASTA amino acid sequence and pKa values for. Allows consideration of post-translational modifications.
http://www.nihilnovus.com/Palabra.html
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» JAligner
Open source Java implementation of the dynamic programming algorithm Smith-Waterman for biological local pairwise sequence alignment.
http://jaligner.sourceforge.net/
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» Jpred
Secondary protein structure prediction from amino acid sequence; based on a consensus from several methods including DSC, PHD, NNSSP, PREDATOR, ZPRED, and MULPRED.
http://www.compbio.dundee.ac.uk/~www-jpred/
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» 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.
http://salilab.org/modbase
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» MSDmotif
Service for protein sequence motifs detection. Search based on the small 3D motifs defined by J.Milner-White.
http://www.ebi.ac.uk/msd-srv/msdmotif/
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» 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.
http://au.expasy.org/melanie/
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» 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).
http://mbt.biobitfield.com/
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» Molecules To Go
Search engine for visualizing 3-D biomolecular models. From the Center for Molecular Modeling, NIH, Maryland.
http://molbio.info.nih.gov/cgi-bin/pdb/
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» 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.
http://bioinfo3d.cs.tau.ac.il/MultiProt/
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» NUMODs Motifs Finder
Finds Nuclease-Associated Modular DNA-binding Domains (NUMODs) in protein sequences
http://bioinfo.weizmann.ac.il/~naaman1/NUMODs/
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» PDB Ligand Environment
Ligand search engine to EBI Macromolecule Structure Database. Provides PDB ID codes with further visualization and statistics charts.
http://www.ebi.ac.uk/msd-srv/msdsite
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» 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.
http://dragon.bio.purdue.edu/pfp/
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» PredictProtein Server
Most widely used server for analysing protein sequences, searching protein databases, and predicting protein structure - from Columbia Univ.
http://cubic.bioc.columbia.edu/predictprotein/
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» 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.
http://www.cbs.dtu.dk/services/ProtFun/
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» 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.
http://bioinf.cs.ucl.ac.uk/psipred/
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» Protein Structure Prediction Using Web Resources
SPORes is a website for protein structure prediction using the web browser as an interface to software that runs of web servers or other resources available over the world wide web.
http://cgat.ukm.my/spores/
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» Proteomics Tools
Online software for protein analysis from the Swiss Institute of Bioinformatics (SIB).
http://www.expasy.org/tools/
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» Protonet
Provides automatic hierarchical classification of proteins sequences.
http://www.protonet.cs.huji.ac.il
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» 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.
http://mericity.com/
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» 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.
http://www.ebi.ac.uk/msd-srv/ssm
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» 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
http://www.ebi.ac.uk/swissprot/
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» Swiss-Model
Automated comparative protein modelling server to make protein modelling accessible to biochemists and molecular biologists worldwide - from GlaxoWellcome Experimental Research, Geneva, Switzerland.
http://swissmodel.expasy.org//SWISS-MODEL.html
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» 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.
http://au.expasy.org/spdbv/
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» 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.
http://www.gene-regulation.com/pub/databases.html#transfac
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» 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 se
http://pir.georgetown.edu
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» 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.
http://www.pir.uniprot.org/
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» Wurst
A protein threading server using sequence profiles combined with a protein sequence to structure compatibility function based on Bayesian statistics.
http://www.zbh.uni-hamburg.de/wurst
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» iMolTalk
Provides protein structure information such as structural alignment, residue contact, protein-protein interfaces, contact maps and general information extraction.
http://i.moltalk.org
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