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http://www.pir.uniprot.org/ - http://www.pir.uniprot.org/
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. |
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InterPro - The Integrated Resource of Protein Domains and Functional Sites. - http://www.ebi.ac.uk/interpro/
A database built from Pfam, PRINTS and PROSITE. |
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The Protein Information Resource - http://pir.georgetown.edu
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. |
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Proteomics Tools - http://www.expasy.org/tools/
Online software for protein analysis from the Swiss Institute of Bioinformatics (SIB). |
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Combinatorial Extension of Polypeptides - http://cl.sdsc.edu/ce.html
Method for finding 3-D similarities in protein structures from the UCSD Supercomputer Center. |
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SWISS-PROT + TrEMBL - http://www.ebi.ac.uk/swissprot/
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. |
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Munich Information Center for Protein Sequences (MIPS) - http://mips.gsf.de/
Bioinformatics research group offering organism specific information (Yeast, Cress) as well as search tools for public databases. |
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Swiss-Pdb Viewer - http://au.expasy.org/spdbv/
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. |
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Protein Structure Prediction Server (PSIPRED) - http://bioinf.cs.ucl.ac.uk/psipred/
3D protein structure prediction from amino acid sequence. Includes MEMSAT for transmembrane topology prediction, GenTHREADER and mGenTHREADER for fold recognition. |
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PredictProtein Server - http://cubic.bioc.columbia.edu/predictprotein/
Most widely used server for analysing protein sequences, searching protein databases, and predicting protein structure - from Columbia Univ. |
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Dali server - http://www.ebi.ac.uk/dali/
The Dali server is a network service for comparing protein structures in 3D. |
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Melanie II 2-D Analysis Software - http://au.expasy.org/melanie/
Powerful, state-of-the-art, 2-D analysis software package with user-friendly interface from the Swiss Institute of Bioinformatics. |
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TRANSFAC-The Transcription Factor Database - http://www.gene-regulation.com/pub/databases.html#transfac
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. |
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Phyre- Protein Homology/analogY Recognition Engine - http://www.sbg.bio.ic.ac.uk/phyre/
Phyre is a free for academics service for predicting the 3-dimensional structure of a protein amino acid sequence. |
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http://www.ebi.ac.uk/msd-srv/ssm - http://www.ebi.ac.uk/msd-srv/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. |
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ELM - Functional Sites in Proteins - http://elm.eu.org
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. |
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BioInfoBank Meta Server - http://meta.bioinfo.pl/submit_wizard.pl
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. |
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http://dis.embl.de - http://dis.embl.de
Computational tool for sequence based prediction of intrinsic protein disorder and unstructured regions within a protein. |
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http://consurf.tau.ac.il/overview.html - http://consurf.tau.ac.il/overview.html
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. |
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Protonet - http://www.protonet.cs.huji.ac.il
Provides automatic hierarchical classification of proteins sequences. |
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http://www.compbio.dundee.ac.uk/~www-jpred/ - http://www.compbio.dundee.ac.uk/~www-jpred/
Secondary protein structure prediction from amino acid sequence; based on a consensus from several methods including DSC, PHD, NNSSP, PREDATOR, ZPRED, and MULPRED. |
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TopMatch: Protein Structure Comparison - http://topmatch.services.came.sbg.ac.at
Public web service for the alignment and superposition of protein structures and the instant visualization of structural similarities. |
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MSDmotif - http://www.ebi.ac.uk/msd-srv/msdmotif/
Service for protein sequence motifs detection. Search based on the small 3D motifs defined by J.Milner-White. |
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ESyPred3D - http://www.fundp.ac.be/urbm/bioinfo/esypred/
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. |
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iMolTalk - http://i.moltalk.org
Provides protein structure information such as structural alignment, residue contact, protein-protein interfaces, contact maps and general information extraction. |
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PDB Ligand Environment - http://www.ebi.ac.uk/msd-srv/msdsite
Ligand search engine to EBI Macromolecule Structure Database. Provides PDB ID codes with further visualization and statistics charts. |
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http://www.zbh.uni-hamburg.de/wurst - http://www.zbh.uni-hamburg.de/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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3D-JIGSAW - http://www.bmm.icnet.uk/~3djigsaw/
Automated comparative (homology) protein modelling, including an interactive mode which highlights known domains and allows users to select and align templates. |
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http://salilab.org/modbase - http://salilab.org/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. |
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http://www.cbs.dtu.dk/services/ProtFun/ - http://www.cbs.dtu.dk/services/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. |
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The ProCKSI Server: Protein Comparison, Knowledge, Similarity and Information - http://www.procksi.net
ProCKSI is a decision support system for protein structure comparison. It provides tools for visualising, analysing, clustering and comparing results. |
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Molecules To Go - http://molbio.info.nih.gov/cgi-bin/pdb/
Search engine for visualizing 3-D biomolecular models. From the Center for Molecular Modeling, NIH, Maryland. |
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JAligner - http://jaligner.sourceforge.net/
Open source Java implementation of the dynamic programming algorithm Smith-Waterman for biological local pairwise sequence alignment. |
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COLORADO3D - http://asia.genesilico.pl/colorado3d/
Service to aid visualisation of potential errors in protein structures. Free for academic users. |
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MultiProt - http://bioinfo3d.cs.tau.ac.il/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. |
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NUMODs Motifs Finder - http://bioinfo.weizmann.ac.il/~naaman1/NUMODs/
Finds Nuclease-Associated Modular DNA-binding Domains (NUMODs) in protein sequences |
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Quaternary Structure Prediction - http://mericity.com/
An experimental bioinformatics server. Classifies protein sequences as homodimers or non-homodimers. Applications: metabolic reconstruction, protein structure and function assignment, and drug-design. |
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Molecular Biology Tools Online - http://mbt.biobitfield.com/
Includes WebOligoMelt (Annealing temperature of oligonucleotides), Virtual Ribosome (translate nucleotide sequences into peptides), and SeqScanGraph (graph melting temperature along nucleotide chain). |
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PFP: Automated Function Prediction Server - http://dragon.bio.purdue.edu/pfp/
Accepts a single query protein sequence and returns the most probable Gene Ontology functional annotations in each of the three ontologies. |
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3D-PSSM Fold Recognition - http://www.sbg.bio.ic.ac.uk/~3dpssm/
Combines sequence and structural information for predicting the structure and/or function of your protein sequence, and can detect remote homologies beyond PSI-Blast. |