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This page provides links relating to protein
characterisation and annotation that have been selected to aid epitope prediction
and analysis. Please note, links open in a separate browser window.
Please feel free to submit your favourite link(s)
by email message to feedback@epitope-informatics.com, which will
be assessed
for inclusion below.
Also, we perform regular checks for broken links, but
please report any links that are broken or in need of update to feedback@epitope-informatics.com.
Links
list update
Link additions made: 20 October 2017
Full correction of any broken and dead links last performed:
18 November 2016.
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INFLUENZA EPITOPE RESOURCES
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Antibody production
Antibody locator resources
Epitope databases and related tools
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AntiJen - A kinetic, thermodynamic and cellular database v2.0
(T and B cell epitopes) |
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Bcipep - A database of B cell epitopes (Bioinformatics Centre,
Institute of Microbial Technology, India). |
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HLA
peptide binding predictions Online facility from
Bioinformatics and Molecular Analysis Section (BIMAS), NIH. |
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IEDB -
The Immune Epitope Database and Analysis
Resource (T and B cell epitopes; NIAID/NIH). |
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IMGT - ImMunoGeneTics
information system specialising in MHC, Ig and TcR molecules from all
vertebrate species. |
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MHCBN v4.0 - a curated database of MHC/TAP binding, non-binding
peptides and T-cell epitopes (Bioinformatics Centre, Institute of
Microbial Technology, India). |
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MHCPred
- Prediction of peptide-MHC class I binding using artificial neural
networks (Center for Biological Sequence Analysis (CBS), Technical
University of Denmark). |
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NetMHC
4.0 -
server predicts binding of peptides to more than 500 HLA-DR alleles
using artificial neural networks (Center for Biological Sequence
Analysis (CBS), Technical University of Denmark). |
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NetMHCIIpan 2.0 -
server predicts binding of peptides to more than 500 HLA-DR alleles
using artificial neural networks (Center for Biological Sequence
Analysis (CBS), Technical University of Denmark). |
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ProPred -
MHC class II epitope prediction server (Bioinformatics Centre, Institute of Microbial
Technology, Chandigarh, India). |
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ProPred I
- Online facility; MHC class I binding peptide prediction
(Bioinformatics Centre, Institute of Microbial Technology, India). |
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SDAP -
Structural Database of Allergenic Proteins (Department of Biochemistry
and Molecular Biology, University of Texas Medical Branch). |
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SYFPEITHI - database of MHC ligands and peptide motifs
(Biomedical Informatics (BMI), Heidelberg/Department of Immunology,
University of Tubingen). |
Protein 3-D structure prediction
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3D-JIGSAW - Server builds 3-D protein models based on homologues
of known structure;
Biomolecular Modelling Laboratory, Cancer Research UK, London. |
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3D structure prediction
- Comprehensive links resource at VLS3D.com (Virtual ligand screening). |
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Center for Molecular Modeling
(CMM) (NIH). |
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CPHmodels
-Protein homology modeling server (Center for Biological Sequence
Analysis, (CBS), Technical University of Denmark). |
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ESyPred3D -
Homology
modelling server that uses MODELLER (see
below) for building final protein 3-D structure (University of Namur,
Belgium). |
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EVA -
Continuous automatic monitoring of protein structure prediction servers
in 'real time'. |
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Interactome3D - Unique homology modelling resource for mapping
structural information onto any protein-protein interaction dataset
dynamically in real-time (Institute for Research in Biomedicine,
Barcelona). |
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MMDB
(Molecular Modeling DataBase) - 3-D structure database for molecular
modelling (NCBI). |
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MODELLER
- Protein modelling by satisfaction of spatial restraints
(Network Science - NetSci). |
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Phyre2 - Phyre2 (Protein Homology/analogY Recognition Engine) remote
homology modeling server (Structural Bioinformatics Group, Imperial
College, London). |
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Protein
Model Portal (PMP) -
Gateway to to various interactive services for model building, and
quality assessment (Computational Structural Biology Group, SIB). |
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Protein Structure Prediction Center (University of California, Davis). |
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ROBETTA
- Full-chain protein structure prediction server from
providers of
Rosetta software (Baker
Lab, University of Washington). |
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SWISS-MODEL -
A fully automated ExPASy protein structure homology modelling server (a good site
for beginners). This server is also accessible from the downloadable
program DeepView
(Swiss-PDBViewer). |
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TINKER - Software tools
for molecular design. |
Protein structure
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Allosteric
Database (ASD) - Database of allosteric proteins and modulators (Molecular
Design Laboratory, Shanghai Jaiotong University, China). |
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Atlas
of Protein Side-Chain Interactions - protein-protein and protein-DNA;
The Biomolecular Structure and Modelling group, University
College London). |
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Blue Gene Project
- Supercomputing applied to protein structure (IBM) |
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CLICK - Topology independent comparison of biomolecular 3-D
structures (Bioinformatics Institute A*STAR, Singapore). |
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Dali server - Online facility for comparing protein 3-D structures
(Institute of Biotechnology, University of Helsinki). |
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Database of Macromolecular Movements
- with associated tools for flexibility and geometric analysis (Gerstein Lab, Yale
University). |
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DNA-binding protein structural families - Hyperlinked information
grouped by DNA recognition motif (The Biomolecular Structure and Modelling group, University
College London). |
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EDS - The
Electron Density Server (Uppsala University, Sweden). |
  |
ELM - The Eukaryotic
Linear Motif resource for protein functional site prediction from input
sequence (ELM consortium). |
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Enzyme
Structures Database - EC®PDB;
database of known enzyme structures deposited in the Protein Data Bank
(PDB). |
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Epitome - Database of structurally inferred antigenic epitopes in
proteins. |
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iELM - The
interactions of Eukaryotic
Linear Motif resource predicts short linear motifs (SLiMs) associated
with protein-protein interaction interfaces (EMBL). |
  |
Interactome3D - A web service for the structural annotation of
protein-protein interaction networks (Institute for Research in
Biomedicine, Barcelona). |
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JenaLib
Jena Library of Biological Macromolecules. Protein atlas; visualization
and analysis resource (Institute of Molecular Biology (IMB), Jena,
Germany). |
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MMDB
(Molecular Modeling DataBase) - 3-D structure database for molecular
modelling (NCBI). |
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ModBase
- Database of Comparative Protein Structure Models (Sali Lab, University
of California, San Francisco). |
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PartsList -
resource for analysing protein folds (Gerstein Lab, Yale University). |
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PDBsum -
A major Internet resource for protein structural information (EMBL-EBI). |
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PDBWiki -
A community annotated knowledge base of biological molecular structures. |
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PISA (PDBePISA) - Protein Interfaces, Surfaces and Assemblies tool,
and prediction of probable quaternary structures (EMBL-EBI). |
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PRINTS - A compendium of protein fingerprints, a group
of conserved motifs used to characterise a protein family. |
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Motif Scan -
ProSite profile and pattern motifs, and Pfam protein families (SIB -
ISREC). |
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PROSITE database of protein
domains, families and functional sites (ExPASy - SIB). |
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Protein Data Bank (PDB)
- From the Research Collaboratory for Structural Bioinformatics (RCSB). |
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Protein Data Bank
in Europe (PDBe) - European resource for the collection,
organisation and dissemination of data on biological macromolecular
structures (EMBL-EBI). |
  |
Protein Data Bank Japan (PDBj) -
Database of macromolecular structures and integrated tools (National
Bioscience Database Center and Osaka University). |
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Protein
Model Portal (PMP; formerly PSI Protein Structure Knowledgebase) -
Gateway to models of a particular protein computed by various
comparative modelling methods (Computational Structural Biology Group,
SIB). |
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Ramachandran
plot - Server displaying main chain torsion angles from an input
protein of known structure (Supercomputer Education and Research Centre, Bangalore). |
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SALIGN
- A multiple protein sequence/structure alignment server based on use of
MODELLER (see previous section) (Sali Lab, University of California, San
Francisco). |
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SWISS-MODEL
Repository - Database of annotated 3-D comparative protein structure
models generated by the ExPASy modelling pipeline SWISS-MODEL (see
preceding section). |
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Theseus -
Simultaneous superimposition of multiple macromolecular structures using
a novel method of maximum likelihood superposition that does not discard
alignment gaps (Brandeis University, Massachusetts). |
Protein
families and domains
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CATH Protein Structure Classification Database
- Searchable database of protein structures in PDB classified by domain
structure and superfamily
(Orengo Group, University College, London). |
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Combinatorial
Extension (CE) Facility for comparing and aligning protein
structures (RCSB PDB). |
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Conserved Domain Database (CDD) and
protein search facility (NCBI). |
  |
Dali
Protein structure alignment
either to another protein structure (pairwise comparison)
or to all entries in the PDB (University of Helsinki, Finland). Dali
pairwise structure alignment also available
here at EMBL-EBI. |
  |
DBAli A database
of protein structure alignments (Sali Lab, University of California, San
Francisco). |
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FATCAT - Flexible
structure AlignmenT by Chaining Aligned
fragment pairs allowing Twists (Sanford-Burnham Medical Research
Institute, US). |
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InterPro
Combines data from PROSITE, PRINTS, PFAM, PRODOM, SMART and
other databases to classify proteins into families and predict domains
and functional sites (EMBL-EBI). |
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PASS2 -
Protein Alignments organised as Structural Superfamilies
(National Centre for Biological Sciences (NCBS), Bangalore, India). |
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PDBeFold
Secondary Structure Matching (SSM) service for the interactive
comparison, alignment and superposition of protein structures in 3-D
(EMBL-EBI). |
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PeCoP -
Server that looks for Persistently Conserved Positions in sequences of
close and distant protein family members. |
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Pfam -
Protein families database of alignments and hidden Markov models (EMBL-EBI). |
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POSA
(Partial Order Structure Alignment). Multiple flexible structure
alignment using partial order graphs. |
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ProDom
- Protein domain families database automatically generated from the
UniProt Knowledge Database. |
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SCOP (Structural
Classification of Proteins) - Protein domain database providing a broad
survey of all known protein folds, and detailed information about close
relatives of any particular protein
(MRC Laboratory of Molecular Biology, Cambridge, UK). |
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SMART
(Simple Molecular Architecture
Research Tool) - Protein domain database and sequence analysis facility
(EMBL). |
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TOPSCAN
A rapid method for comparing protein structures based on their secondary
structures (University College London, UK). |
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VAST
Vector Alignment Search Tool for detecting
similar protein 3-D structures, and distant homologues that escape
detection by sequence comparison (NCBI). |
Protein signal/sorting sequence prediction
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PSORT - Prediction of
protein sorting signals and localization sites in amino acid sequences. |
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SignalP - Prediction
of signal peptide cleavage sites in protein sequences (Center for Biological Sequence Analysis, (CBS), Technical University of Denmark). |
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SOSUIsignal
Signal peptide prediction server
(Department of Biotechnology, Tokyo University of Agriculture and
Technology). |
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TargetP
- Predicts subcellular location of eukaryotic proteins (Center for
Biological Sequence Analysis, (CBS), Technical University of Denmark). |
Membrane
proteins and topology prediction
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DAS - DAS (Dense
Alignment Surface method) Transmembrane
prediction server (Stockholm Bioinformatics Center). |
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HMMTOP -
Server for predicting transmembrane helices and protein topology (hosted by Hungarian Academy of Sciences). |
  |
Membrane Protein Data Bank (MPDB)
- Database containing select structural and functional information on
membrane proteins and peptides (Trinity College Dublin). |
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Membrane Protein Resources
(Stephen White laboratory, University
of California, Irvine). |
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Membrane Proteins of Known 3D Structure - continuously updated list from the Stephen White laboratory, University
of California, Irvine. |
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Orientations of
Proteins in Membranes (OPM) - Database providing topologies of
membrane proteins relative to the lipid bilayer of the hydrocarbon core
(Mosberg Lab, University of Michigan, US). |
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orienTM -
Predicts orientation (topology) of transmembrane proteins from sequence (hosted
by University of Athens). |
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Protein Data Bank of Transmembrane Proteins (PDBTM)
A comprehensive and updated database of transmembrane proteins in the
PDB (Institute of Enzymology, Hungarian Academy of Science). |
  |
SOSUI
- Classification and secondary structure prediction of membrane proteins
(Department of Applied Physics, Nagoya University, Japan). |
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TMHMM
- Prediction of transmembrane helices in proteins (Center for Biological
Sequence Analysis, (CBS), Technical University of Denmark). |
  |
TMpred
- Prediction of transmembrane regions and orientation (Swiss Institute
of Bioinformatics). |
  |
TopPred - Topology prediction of membrane proteins (Institut
Pasteur). |
Protein
coiled coils
  |
COILS -
Prediction of protein coiled coil regions (Swiss Institute of
Bioinformatics). |
  |
MARCOIL
- Hidden Markov Model-based program for predicting protein coiled coil
domains. (Bioinformatics, Walter and Eliza Hall
Institute of Medical Research, Australia). |
  |
MultiCoil
- Prediction of dimeric and trimeric protein coiled coils (MIT Computer
Science and Artificial Intelligence Laboratory (CSAIL)). |
  |
PairCoil2 -
Prediction of coiled coil regions in non-multimeric proteins (MIT -
CSAIL). |
Proteolytic enzymes
  |
A
Protein Degradation Resource (Wilkinson Lab, Emory University School
of Medicine, Atlanta, US). |
  |
AAA
- ATPases Associated with various cellular Activities protein superfamily
- information and links (Institute of Molecular Biosciences, Graz,
Austria. |
  |
CutDB -
Database resource focusing on the annotation of actual and predicted individual proteolytic events (Sanford-Burnham
Medical Research Institute, US). |
  |
EC-IUBMB Peptidase
nomenclature: lists a and
b. |
  |
HIV Protease Database
(National Institute of Standards and Technology (NIST), US). |
  |
International Proteolysis Society
(IPS). |
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MEROPS -
Peptidase database (Wellcome Trust Sanger Institute, UK). |
  |
NetChop -
Neural network-based proteasome cleavage site prediction server (Center
for Biological Sequence Analysis, (CBS), Technical University of
Denmark). |
  |
PAProC - Proteasome cleavage
site prediction facility (Departments of Immunology and Biomathematics,
University Tubingen. |
  |
PeptideCutter -
Protease cleavage site predictor (ExPASy- SIB). |
  |
PoPS -
Computational tools for predicting and modelling protease specificity
(Victorian Bioinformatics Consortium-Monash University, Australia. |
Selected other specialist protein
families
  |
Androgen Receptor
Gene Mutations Database (Lady Davis Institute for Medical Research,
McGill University, Canada). |
  |
CAZy - Carbohydrate-Active
enZYmes knowledgebase focusing on enzymes that degrade, modify or create
glycosidic bonds (AFMB
- CNRS - University of Aix-Marseille). |
  |
Cytokines
& Cells Online Pathfinder
Encyclopaedia (COPE). |
  |
Directory of
P450-containing Systems (International Centre for Genetic
Engineering and Biotechnology, Trieste, Italy). |
  |
DOLOP
- A Database Of bacterial LipOProteins (MRC Laboratory of Molecular
Biology, Cambridge, UK). |
  |
EF-hand Calcium-Binding Proteins Data Library (Center for Structural
Biology, Vanderbilt University, US). |
  |
EPD
- The Eukaryotic Promoter Database (SIB). |
  |
GPCRDB
(G Protein-Coupled Receptor Data Base) - Knowledgebase resource for G protein-coupled
receptors (Centre for Molecular and Biomolecular Informatics, the
Netherlands). |
  |
IMGT (ImMunoGeneTics)
- Immunogenetics and immunoinformatics knowledgebase resource and tools. |
  |
Kinase.com -
Genomics, evolution and function of protein kinases resource (Gerard
Manning lab, Salk Institute, California). |
  |
Kinesin Home Page
- Resource for kinesin and related proteins (Department of Cell Biology,
Duke University, US). |
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Myosin Home Page
(MRC Laboratory of Molecular Biology, Cambridge, UK). |
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Phospho.ELM - Database of S/T/Y phosphorylation sites (EMBL). |
  |
Plasma
Proteome Database (PPD) - Online resource for human plasma proteins
and isoforms (Pandey Lab, Johns Hopkins University/Institute of
Bioinformatics, India/HUPO). |
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PPAR Resource Page
- Information site for the Peroxisome Proliferator-Activated Receptors
(Penn State University, US). |
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Protein
Kinase Resource (PKR) |
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REBASE
The Restriction Enzyme Database (hosted by New England BioLabs Inc.). |
  |
Ribosomal Database
Project (RDP) Ribosome related knowledgebase and tools (Michigan
State University, US). |
Proteomics
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ABRF list of commercial
protein analysis facilities (The Association of Biomolecular Resource Facilities). |
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ABRF
Proteomics Research Group. |
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Australian Proteome
Analysis Facility (APAF). |
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Biochemical Pathways - ExPASy. |
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BRENDA (BRaunschweig
ENzyme DAtabase) - enzyme data and metabolic information. |
  |
British Society for
Proteome Research (BSPR) |
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Database of Interacting
Proteins (DIP; University of California). |
  |
Delta Mass
Database of Protein Post Translational Modifications
(ABRF). |
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ENZYME - Enzyme nomenclature
database (ExPASy). |
  |
Enzyme nomenclature
(International Union of Biochemistry and Molecular Biology (IUBMB)). |
  |
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. |
  |
The Human Proteome
Project (HPP) - an international project organized by the
Human Proteome
Organization (HUPO) aiming to characterise all 20,300 known genes of
the human genome. |
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InterPro - database of
protein families, domains and functional sites (EBI). |
  |
KEGG - Kyoto Encyclopedia of Genes and Genomes
(Bioinformatics Center, Kyoto University). |
  |
massXpert
- program for predicting and analysing protein/peptide MS data (Filippo Rusconi, University of Bordeaux, France). |
  |
OMICtools - a
community search platform for finding, discussing and sharing tools for
biological data analysis. |
  |
Plasma
Proteome Database (PPD) - Online resource for human plasma proteins
and isoforms (Pandey Lab, Johns Hopkins University/Institute of
Bioinformatics, India/HUPO). |
  |
PRIDE PRoteomics IDEntifications Database (EMBL-EBI). |
  |
The Protein Data Bank (PDB) (Research
Collaboratory for Structural Bioinformatics (RCSB)). |
  |
Protein Information Resource (PIR)
- Protein informatics resource (sequence databases and structural information) for proteomics,
genomics & systems biology
research. |
  |
Protein-Protein interaction: Docking, Hotspot, Network
- Comprehensive links resource at VLS3D.com (Virtual ligand screening). |
  |
The Protein Society
- promotes communication,
cooperation, and collaboration among scientists involved in the study of
proteins through international forums. |
  |
ProteomeBinders
European consortium establishing a comprehensive infrastructure resource
of binding molecules for detecting the human proteome (including antibodies, alternative protein scaffolds, nucleic acids
and peptides). |
  |
Proteomics
resources
- ExPASy (Expert Protein Analysis System). |
  |
RefSeq
- The NCBI Reference Sequence resource. |
  |
RIKEN Structural
Genomics/Proteomics Initiative (RSGI) - The Institute of Physical and
Chemical Research, Japan. |
  |
spectroscopyNOW.com - proteomics portal with a spectroscopy focus,
from Wiley (publishers). |
  |
Swiss Proteomics Society
(SPS). |
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UniProt (Universal Protein Resource) - a central repository of
protein sequence and function information from
UniProtKB/Swiss-Prot,
UniProtKB/TrEMBL and
PIR protein databases. |
Computational biology/Bioinformatics
  |
Bioinformatics
@ Manchester University of Manchester (UK). |
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BioInformatics and Molecular
Analysis Section (BIMAS) - Center for Information Technology (CIT), NIH. |
  |
Bioinformatics.ca (Canadian
bioinformatics portal). |
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Bioinformatics Centre (National
University of Singapore). |
  |
Bioinformatics
Institute of India - non-profit; educational, research and
development centre. |
  |
Canadian Bioinformatics.ca Links Directory - a dynamic-featured list
of bioinformatics resources that also lists all links contained in the
NAR Webserver issue. |
  |
Bioinformatics Organisation - Provides free, open resources for research, development and education. |
  |
Centre for Molecular and Biomolecular Informatics (CMBI) -
University of Nijmegen, the Netherlands. |
  |
Computational Biology Center (IBM). |
  |
Computational Cancer
Genomics (CCG) group of the
Swiss Institute of
Bioinformatics (SIB) - Development of analysis tools and databases
relating molecular sequences and biological functions. |
  |
Db Browser -
(Bioinformatics, University of Manchester). |
  |
European Bioinformatics Institute
(EMBL-EBI). |
  |
Global
Organisation for Bioinformatics Learning, Education & Training (GOBLET)
portal. |
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Institute of Bioinformatics and Biotechnology (IBB)
- University of Pune, India). |
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International Society for Computational
Biology (ISCB). |
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Mathematical, Computational and Systems Biology (MCSB;
University of California, Irvine). |
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National Center for Biotechnology
Information (NCBI) - US National Library of Medicine (NLM). |
  |
Shanghai Center for
Bioinformation Technology (SCBIT) |
  |
South African National Bioinformatics
Institute (SANBI) - University of the Western Cape. |
  |
Swiss Institute of Bioinformatics
(SIB). |
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The Open Bioinformatics
Foundation (O|B|F) - non-profit, volunteer-run organisation focused
on supporting open-source programming in bioinformatics. |
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Copyright © 2020 ePitope Informatics
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Consensus epitope prediction
(Human DNA
repair protein,
MGMT - peak
epitope residues
shown in gold).

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