Links - ePitope Informatics - epitope prediction and protein analysis

This page provides a selection of links relating to protein analysis and annotation including epitope prediction. Links open in a separate browser window.

Please feel free to submit your favourite link(s), which we will assess for inclusion here. Also, we perform regular checks for broken links, but if you find any links are broken please report them to feedback@epitope-informatics.com.

INFLUENZA AND EPITOPE RESOURCES - 27 April 2009

In the light of very recent developments regarding swine influenza, we provide the following links to influenza and relevant epitope resources:

Influenza and epitopes database and tools at BioHealthBase (BioDefence and Public Health Database); National Institute of Allergy and Infectious Diseases (NIAID).
Influenza Virus Resource: Information, Search and Analysis
at National Center for Biotechnology Information (NCBI).
Influenza Sequence and Epitope Database (ISED) at Korea National Institute of Health (KNIH) and Korea University (KU)

Influenza Virus Database (IVDB) at Beijing Institute of Genomics (BIG).

Pathogen Portal to the Bioinformatics Resource Centers (BRCs)
sponsored by the National Institute of Allergy and Infectious Diseases (NIAID).

Links update - 29 April 2009

We have updated links, including adding new links to the following sections:

Proteolytic enzymes

Bioinformatics

Protein structure

Proteomics

Further links revision work is on-going.

HUMAN PROTEIN ATLAS

The Human Protein Atlas is an open, freely accessible resource for
systematic exploration of the human proteome characterised by
antibody proteomics (courtesy of The Swedish Human Proteome
Resource (HPR) program). Antibodies are used for protein profiling,
and the Human Protein Atlas shows expression and localization of
proteins in a wide variety of normal human tissues and cancer cells,
and is part of the HUPO Human Antibody Initiative (HAI).

ePitope Informatics listed in Nature feature articles:

"Bioinformatics: Data's future shock" (Nature, 15
April 2004, vol. 428, p774).
"Bioinformatics: Programmed for success" (Nature, 11
September 2003, vol. 425, p209).

"Bioinformatics: Bringing it all together" (Nature, 17
October 2002, vol. 419, p761).

Proteomics

	Aberdeen Proteome Facility - Proteomics services for academic and commercial users, University of Aberdeen, Scotland.
	Abnova - Company specialising in high throughput antibody production for proteomics.
	ABRF list of commercial protein analysis facilities.
	ABRF Proteomics Research Group.
	Australian Proteome Analysis Facility (APAF).
	Biochemical Pathways - ExPASy.
	BRENDA (BRaunschweig ENzyme DAtabase) - enzyme data and metabolic information.
	British Society for Proteome Research (BSPR)
	Centre for Proteomic Research - University of Southampton, UK.
	Database of Interacting Proteins (DIP; hosted by UCLA).
	Delta Mass at the ABRF (Assoc. of Biomolecular Resource Facilities) - Database of Protein Post Translational Modifications.
	ENZYME - Enzyme nomenclature database (ExPASy).
	Enzyme nomenclature (International Union of Biochemistry and Molecular Biology (IUBMB)).
	FingerPrints Proteomics Facility - University of Dundee, Scotland.
	Gepasi - a software package for modeling biochemical systems
	HUGE - Human Unidentified Gene-Encoded large proteins database (Kazusa cDNA project).
	Human Protein Atlas Public resource for systematic exploration of the human proteome with antibody proteomics (The Swedish Human Proteome Resource (HPR) program). Antibody atlas shows the expression and localization of proteins in a large variety of normal human tissues and cancer cells.
	Human Protein Interaction Database (HPID) at Inha University, Korea.
	Human Proteome Initiative (HPI) - ExPASy.
	Human Proteome Folding Project (Institute for Systems Biology (ISB)).
	Integr8 Database (Access to complete genomes and proteomes - EBI).
	International Protein Index (IPI) at EBI.
	InterPro - database of protein families, domains and functional sites (EBI).
	KEGG - Enzymes and metabolic PATHWAY databases at KEGG (Kyoto Encyclopedia of Genes and Genomes; Bioinformatics Center, Kyoto Univ.).
	massXpert - program for predicting and analysing protein/peptide MS data (Filippo Rusconi, University of Bordeaux, France).
	MDS Proteomics - proteomics-based drug discovery company.
	NCBI Entrez protein sequence retrieval facility.
	Northeast Structural Genomics Consortium (NESG) - selected links.
	PRIDE PRoteomics IDEntifications Database (EMBL-EBI).
	The Protein Data Bank (PDB) (Research Collaboratory for Structural Bioinformatics (RCSB)).
	ProteinEducation.org - The Protein Society.
	Protein Information Resource (PIR) - Protein sequence databases and structural information for proteomics research.
	Protein-Protein Interaction Database (PPID).
	Protein Reviews on the Web (PROW).
	Protein Structure Initiative (PSI) - National Institute of General Medical Sciences (NIGMS), NIH.
	Proteome Database (Proteome, Inc.) - service requires site registration and subscription.
	Proteome Society.
	ProteomeBinders European consortium proposing to establish a comprehensive infrastructure resource of binding molecules for detection of the human proteome (antibodies, alternative protein scaffolds, nucleic acids, peptides and chemical entities are planned to be evaluated).
	Proteomics tools - ExPASy (Expert Protein Analysis System).
	RefSeq - The NCBI Reference Sequence project.
	RIKEN Structural Genomics/Proteomics Initiative - The Institute of Physical and Chemical Research, Japan.
	Sir Henry Wellcome Functional Genomics Facility - Proteomics services, University of Glasgow, Scotland.
	spectroscopyNOW.com - proteomics portal with a spectroscopy focus, from Wiley (publishers).
	Swiss Proteomics Society.
	The Technology Facility - Dept of Biology, University of York, U.K.
	The JCB Protein-Protein Interaction Website (PPI).
	UniProt (Universal Protein Resource) - a central repository of protein sequence and function information from Swiss-Prot, TrEMBL and PIR protein databases.
	The Protein Society.
	Web Resources for Protein Scientists (The Protein Society).

Bioinformatics

	Bioinformatics and Computational Biology at UCSC (University of California, Santa Cruz).
	BioInformatics and Molecular Analysis Section (BIMAS) at the NIH.
	Bioinformatics and Pattern Discovery Group (IBM).
	Bioinformatics at the NIH (National Institutes of Health).
	Bioinformatics.ca (Canadian bioinformatics portal).
	Bioinformatics Centre (National Univ. of Singapore).
	Bioinformatics.fr - a global site for sharing knowledge, tips and information related to bioinformatics.
	Bioinformatics Group (ISREC - Swiss Inst. for Experimental Cancer Research).
	Bioinformatics Institute of India - non-profit; educational, research and development centre.
	Bioinformatics Organisation - Provides free, open resources for research, development and education.
	BioInformatics Services (BIS) - biotechnology consultancy firm.
	bioinformatik.de (Yahoo-like bioinformatics Web directory).
	Centre for Molecular and Biomolecular Informatics (CMBI) - University of Nijmegen, the Netherlands.
	Computational Biology Center (IBM).
	Database Browser - (Manchester Bioinformatics - UMBER (see below in this section)).
	European Bioinformatics Institute (EBI; EMBL Outstation).
	GeneBio (Geneva Bioinformatics S.A.) - Proteomics software and commercial licensing arm of SIB (see below).
	Institute of Bioinformatics and Biotechnology (Univ. Pune, India).
	Institute of Cheminformatics Studies (Noida, India).
	International Society for Computational Biology (ISCB).
	Mathematical, Computational and Systems Biology (MCSB; University of California, Irvine).
	National Center for Biotechnology Information (NCBI).
	Penn Center for Bioinformatics (Univ. of Pennsylvania).
	Research Collaboratory for Structural Bioinformatics (RCSB; hosts Protein Data Bank (PDB) and other resources).
	Scottish Bioinformatics Forum (SBForum.org)
	Shanghai Center for Bioinformation Technology (SCBIT)
	South African National Bioinformatics Institute (SANBI; Univ. of the Western Cape).
	Swiss Institute of Bioinformatics (SIB; hosts the ExPASy proteomics server (see above) and other resources).
	The Open Bioinformatics Foundation.
	UCLA Bioinformatics.
	UK Bioinformatics Forum (UKBF; Oxford Universities and Oxfordshire Bioscience Network (OBN) joint venture to promote bioinformatics and networking between academia and industry.
	University of Manchester Bioinformatics (UK).
	VSNS BioComputing Division - online bioinformatics education resource (University of Bielefeld, Germany).
	Young Bioinformaticians Forum (YBF; UK).

Proteolytic enzymes

	A Protein Degradation Resource.
	AAA - ATPases Associated with various cellular Activities - protein superfamily.
	CutDB - A BioMed Central database focusing on the annotation of individual proteolytic events (actual and predicted).
	EC/IUBMB - Peptidase nomenclature: lists a and b.
	HIV Protease Database.
	International Proteolysis Society (IPS).
	MEROPS - protease database.
	NetChop - Online neural network-based proteasome cleavage prediction facility; Centre for Biological Sequence Analysis, Tech. University of Denmark.
	PAProC - Online proteasome cleavage prediction facility.
	Peptidase entries/families in SWISS-PROT - ExPASy.
	PoPS - A software tool for modelling protease activity.

Other specialist protein families

	Androgen Receptor Mutations Database.
	CAZy - Carbohydrate-active enzymes database.
	Cytokines Online Pathfinder Encyclopaedia (COPE).
	Directory of P450-containing Systems.
	DOLOP - A Database Of bacterial LipOProteins, MRC Laboratory of Molecular Biology, Cambridge, UK.
	EF-hand Calcium-Binding Proteins Data Library
	EPD - The Eukaryotic Promoter Database from the SIB.
	Glucocorticoid Receptor Resource (GRR).
	GPCRDB - Information system and database for G protein-coupled receptors (GPCRs).
	IMGT - ImMunoGeneTics information system specialising in MHC, Ig and TcR molecules from all vertebrate species.
	Kinase function, evolution and diversity (Kinase.com).
	Kinesin Motor Proteins Home Page.
	Membrane Protein Data Bank (MPDB)
	Membrane Protein Resources from the Stephen White laboratory, Univ. of California at Irvine.
	Metalloprotein Database and Browser (MDB).
	Myosin Home Page.
	Peroxisome Proliferator-Activated Receptor (PPAR) Resource.
	Phospho.ELM - Database of S/T/Y phosphorylation sites (hosted by EMBL).
	Protein Data BanK of Transmembrane Proteins (PDBTM).
	Protein Kinase Resource (PKR)
	Protein(s) specific databases and resources (links list - ExPASy).
	REBASE: The Restriction Enzyme Database.
	Ribosomal Database Project (RDP).
	Steroid Receptor Associated Proteins Resource (SRAPR).
	The Ligand-Gated Ion Channel Database (LGIC; EBI).
	Thyroid Hormone Receptor Resource (THRR).
	TRANSFAC - eukaryotic transcription factor database from BIOBASE - Biological Databases, Germany.

Protein structure

	Atlas of Protein Side-Chain Interactions (prot-prot and prot-DNA).
	Blue Gene Project (Supercomputing applied to protein structure - IBM)
	Database of Macromolecular Movements - with associated tools for geometric analysis (Gerstein Lab, Yale Univ.).
	EBI Macromolecular Structure Database (EMBL - EBI).
	ELM (The Eukaryotic Linear Motif database) - tools for evaluating protein linear motifs that aim to reduce over-prediction of short functional motifs (cf. PROSITE below; Biocomputing Unit, EMBL).
	Enzyme Structures Database (EC-to-PDB).
	HMMSTR/I-sites/ROSETTA Prediction Server - prediction of protein structure from sequence.
	Library of Protein Family Cores (LPFC).
	Membrane Proteins of Known 3D Structure - continuously updated list from the Stephen White laboratory, Univ. of California at Irvine.
	Molecular Modelling Database (MMDB) of Entrez protein structures at NCBI (National Centre for Biotechnology Information).
	PartsList - resource for analysing protein folds (Gerstein Lab, Yale Univ.).
	PDBsum - A major Internet resource for protein structural information (EBI - Wellcome Trust).
	PQS - Protein Quaternary Structure Query Form (European Bioinformatics Institute)
	PRINTS - Protein Motif Fingerprint Database.
	Motif Scan - ProSite profile and pattern motifs, and Pfam protein families (SIB - ISREC).
	PROMISE - The Prosthetic groups and Metal Ions in Protein Active Sites Database.
	PROSITE database of protein families and domains.
	Protein 3D structure and related databases (links page - ExPASy).
	Protein Data Bank (PDB).
	Protein Data Bank of Transmembrane Proteins (PDBTM).
	Protein Structure Prediction Center (University of California, Davis).
	Ramachandran plot - WWW facility (Bioinformatics Centre, Bangalore, India).
	Rules for 3D protein-DNA interactions (The Biomolecular Structure and Modelling group, University College London).
	SCOP - Structural classification of proteins (LMB (MRC), Univ. Cambridge, U.K.).
	Search PDB for a protein structure.
	Seq-Gen - Software for simulating protein sequence evolution along evolutionary trees (Institute of Evolutionary Biology, University of Edinburgh).
	SitesBase - Dat6abase of known ligand binding sites within the PDB.
	Taxonomy of protein-DNA complex structures. (The Biomolecular Structure and Modelling group, University College London)
	Ten Most Wanted project - protein structure prediction initiative inviting submission to the "ten most wanted" list of proteins for testing prediction algorithms (University of California, Davis).

Protein domains

	CATH Protein Structure Classification Database - database of protein structures classified by structural domains (Department of Biochemistry, University College London).
	Conserved Domain Database (CDD) and CD-Search facility (NCBI).
	Domain Fishing - WWW facility using PFAM, PDB, SCOP and sec. struct. filtering to find protein domains (Biomolecular Modelling Laboratory, Cancer Research UK, London).
	ProDom - Protein domain families database automatically generated from SWISS-PROT and TrEMBL sequence databases.
	Simple Molecular Architecture Research Tool (SMART) - Protein domain database.

Similarities in protein structure

	BLOCKS - database of protein alignment blocks (Fred Hutchinson Cancer Research Center, USA).
	PASS2 - Protein Alignments organised as Structural Superfamilies (National Centre for Biological Sciences (NCBS), Bangalore, India).
	The Dali Database - Families of structurally similar proteins (formerly "FSSP" database).
	Finding 3-D Similarities in Protein Structures (A resource of the San Diego Supercomputer Center (SDSC)).
	PeCoP - WWW facility that finds Persistently Conserved Positions in sequences of close and distant protein family members.
	Pfam - Protein families database of alignments and hidden Markov models (Sanger Institute (Wellcome Trust), UK).
	VAST (Vector Alignment Search Tool) for detecting protein structure neighbours (NCBI).

Protein comparative/homology modelling

	3D-JIGSAW - Server builds 3-D protein models based on structure of known homologues; Biomolecular Modelling Laboratory, Cancer Research UK, London).
	Center for Molecular Modeling (CMM) at the NIH.
	ESyPred3D - WWW homology modelling server that uses MODELLER (see link below) for building final protein 3-D structure.
	MMDB (Molecular Modeling DataBase) - Entrez's 3-D structure database for molecular modelling (NCBI).
	MODELLER Protein modelling by satisfaction of spatial restraints (Network Science).
	ROBETTA Full-chain protein structure prediction server from Rosetta software hosts (Baker Lab, Univ. Washington).
	SWISS-MODEL: An automated comparative protein modelling server (a good site for beginners).
	TINKER - Software tools for molecular design.

Protein signal/sorting sequence prediction

	PSORT WWW Server - Prediction of protein sorting signals and localization sites in amino acid sequences (hosted by University of Tokyo).
	SignalP - WWW Prediction Server (Center for Biological Sequence Analysis, (CBS), BioCentrum-DTU, Technical Univ. of Denmark).
	SIG-Pred - Online signal peptide prediction facility, Bioinformatics Research Group, Univ. Leeds, UK.
	SOSUIsignal (Department of Biotechnology, Tokyo University of Agriculture and Technology).
	SubLoc - Prediction of protein subcellular location (Institute of Bioinformatics, Tsinghua Univ., China).
	TargetP - Prediction of protein subcellular location (Center for Biological Sequence Analysis, Technical Univ. of Denmark).

Protein transmembrane helix prediction

	DAS - DAS (Dense Alignment Surface method) Transmembrane prediction server (Stockholm Bioinformatics Center).
	HMMTOP - Prediction of transmembrane helices and topology of proteins (restricted access to server hosted by Hungarian Acad. of Sciences, Budapest).
	orienTM - Orientation of transmembrane proteins (Univ. of Athens server).
	SOSUI - Classification and secondary structure prediction of membrane proteins (Department of Applied Physics, Nagoya University, Japan).
	TMHMM - Prediction of transmembrane helices in proteins (Center for Biological Sequence Analysis, (CBS), BioCentrum-DTU, Technical Univ. of Denmark).
	TMpred - Prediction of transmembrane regions and orientation (ch.EMBnet.org server).
	TopPred - Topology prediction of membrane proteins (Institut Pasteur server).

Protein coiled coils

	COILS - Online prediction of protein coiled coil regions (Lupas method; ch.EMBnet.org server).
	MARCOIL - a hidden Markov model-based program for predicting protein coiled coil domains. (Genetics and Bioinformatics Group, Walter and Eliza Hall Institute of Medical Research, Australia).
	MultiCoil - Online prediction of two- and three-stranded protein (dimeric and trimeric) coiled coils.
	PairCoil2 - Online prediction of coiled coil regions in proteins (Berger's method).
	Prediction of Coiled Coils from Protein Sequences (Univ. of York).

T cell epitopes and prediction

	AntiJen (formerly JenPep) - Online database of published, experimentally derived data for peptides binding to MHC class I, II and TAP molecules, and a separate T cell epitope database (Bioinformatics Group, The Edward Jenner Inst. for Vaccine Res., Compton, UK).
	EpiBase - Platform for HLA Class I/II epitope prediction and selection with a vaccine development (cancer and infectious diseases) and protein deimmunization focus (AlgoNomics NV, Belgium).
	EPIPREDICT - Software for HLA class II epitope prediction.
	HLA peptide binding predictions Online facility from Bioinformatics and Molecular Analysis Section (BIMAS), NIH.
	IMGT - ImMunoGeneTics information system specialising in MHC, Ig and TcR molecules from all vertebrate species.
	MHCPred - quantitative prediction of peptide binding to major histocompatibility complexes (Bioinformatics Group, The Edward Jenner Inst. for Vaccine Res., Compton, UK).
	ProPred - Online facility; MHC class II epitope prediction based on TEPITOPE virtual matrices (Bioinformatics Centre, Institute of Microbial Technology, India).
	ProPred I - Online facility; MHC class I binding peptide prediction (Bioinformatics Centre, Institute of Microbial Technology, India).
	SYFPEITHI - database of MHC ligands and peptide motifs.

Antibody production

	Antibody Resource Page (ARP).
	Antibody Station.
	IHCWorld.
	Peptide Resource Page (PRP).
	Peptide Forum.
	PIERCE Antibody Production - Useful information, linked to the use of Pierce products.
	The Recombinant Antibody Pages (and Links list) - Tech. Univ. at Brunswick, Braunschweig, Germany).

Antibody locator resources

	AbD-Serotec antibody location service.
	Antibody Explorer - Sigma facility for searching their large antibody collection.
	Antibody Resource Page (ARP).
	Biocompare antibody location service.
	IHCWorld.

This page was last updated:
Sunday May 10, 2009

Refresh page
(if today's date is significantly greater
than that shown above)

epitope prediction
Consensus epitope prediction
(Human DNA
repair protein,
MGMT - peak
epitope residues
shown in gold).

Recommend ePitope Informatics

Click here to tell a colleague about us.

B cell epitope references?

Use us for epitope prediction and protein analysis?