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.
 

 

 
  INFLUENZA EPITOPE RESOURCES

 

Antibody production

Antibody Resource Page (ARP) links.
Bio-Rad Antibody (formerly AbD Serotec) Resources - Antibody related mini-reviews, educational summaries, application notes and blog.
IHCWorld.

Antibody locator resources

AbMiner - Antibody search with antibody validation as a focus (Genomics and Bioinformatics Group, LMP, CCR, National Cancer Institute).
Antibodypedia - an open-access database of commercially available antibodies against human protein targets (part of HUPO's Human Antibody Initiative (HAI) in collaboration with the Nature Publishing Group.
Antibody Explorer - Sigma-Aldrich facility for searching their large antibody collection.
The Antibody Registry - register of uniquely identified antibodies including commercial antibodies from about 200 vendors.
Antibody Resource Page (ARP).
Bioz - A science aggregator providing a comprehensive antibody search and ranking facility from their homepage, and a searchable list of antibody and related categories here.
Biocompare antibody location service.
Human Protein Atlas - Antibody proteomics for systematic exploration of the human proteome.
IHCWorld.
Linscott's Directory of Immunological & Biological Reagents.

Epitope databases and related tools

AntiJen - A kinetic, thermodynamic and cellular database v2.0  (T and B cell epitopes)
Bcipep - A database of B cell epitopes (Bioinformatics Centre, Institute of Microbial Technology, India).
HLA peptide binding predictions Online facility from Bioinformatics and Molecular Analysis Section (BIMAS), NIH.
IEDB - The Immune Epitope Database and Analysis Resource (T and B cell epitopes; NIAID/NIH).
IMGT - ImMunoGeneTics information system specialising in MHC, Ig and TcR molecules from all vertebrate species.
MHCBN v4.0 - a curated database of MHC/TAP binding, non-binding peptides and T-cell epitopes (Bioinformatics Centre, Institute of Microbial Technology, India).
MHCPred - Prediction of peptide-MHC class I binding using artificial neural networks (Center for Biological Sequence Analysis (CBS), Technical University of Denmark).
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).
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).
ProPred - MHC class II epitope prediction server (Bioinformatics Centre, Institute of Microbial Technology, Chandigarh, India).
ProPred I - Online facility; MHC class I binding peptide prediction (Bioinformatics Centre, Institute of Microbial Technology, India).
SDAP - Structural Database of Allergenic Proteins (Department of Biochemistry and Molecular Biology, University of Texas Medical Branch).
SYFPEITHI - database of MHC ligands and peptide motifs (Biomedical Informatics (BMI), Heidelberg/Department of Immunology, University of Tubingen).

Protein 3-D structure prediction

3D-JIGSAW - Server builds 3-D protein models based on homologues of known structure; Biomolecular Modelling Laboratory, Cancer Research UK, London.
3D structure prediction - Comprehensive links resource at VLS3D.com (Virtual ligand screening).
Center for Molecular Modeling (CMM) (NIH).
CPHmodels -Protein homology modeling server (Center for Biological Sequence Analysis, (CBS), Technical University of Denmark).
ESyPred3D - Homology modelling server that uses MODELLER (see below) for building final protein 3-D structure (University of Namur, Belgium).
EVA - Continuous automatic monitoring of protein structure prediction servers in 'real time'.
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).
MMDB (Molecular Modeling DataBase) - 3-D structure database for molecular modelling (NCBI).
MODELLER - Protein modelling by satisfaction of spatial restraints (Network Science - NetSci).
Phyre2 - Phyre2 (Protein Homology/analogY Recognition Engine) remote homology modeling server (Structural Bioinformatics Group, Imperial College, London).
Protein Model Portal (PMP) - Gateway to to various interactive services for model building, and quality assessment (Computational Structural Biology Group, SIB).
Protein Structure Prediction Center (University of California, Davis).
ROBETTA - Full-chain protein structure prediction server from providers of Rosetta software (Baker Lab, University of Washington).
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).
TINKER - Software tools for molecular design.

Protein structure

Allosteric Database (ASD) - Database of allosteric proteins and modulators (Molecular Design Laboratory, Shanghai Jaiotong University, China).
Atlas of Protein Side-Chain Interactions - protein-protein and protein-DNA; The Biomolecular Structure and Modelling group, University College London).
Blue Gene Project - Supercomputing applied to protein structure (IBM)
CLICK - Topology independent comparison of biomolecular 3-D structures (Bioinformatics Institute A*STAR, Singapore).
Dali server - Online facility for comparing protein 3-D structures (Institute of Biotechnology, University of Helsinki).
Database of Macromolecular Movements - with associated tools for flexibility and geometric analysis (Gerstein Lab, Yale University).
DNA-binding protein structural families - Hyperlinked information grouped by DNA recognition motif (The Biomolecular Structure and Modelling group, University College London).
EDS - The Electron Density Server (Uppsala University, Sweden).
ELM - The Eukaryotic Linear Motif resource for protein functional site prediction from input sequence (ELM consortium).
Enzyme Structures Database - ECPDB; database of known enzyme structures deposited in the Protein Data Bank (PDB).
Epitome - Database of structurally inferred antigenic epitopes in proteins.
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).
JenaLib Jena Library of Biological Macromolecules. Protein atlas; visualization and analysis resource (Institute of Molecular Biology (IMB), Jena, Germany).
MMDB (Molecular Modeling DataBase) - 3-D structure database for molecular modelling (NCBI).
ModBase - Database of Comparative Protein Structure Models (Sali Lab, University of California, San Francisco).
PartsList - resource for analysing protein folds (Gerstein Lab, Yale University).
PDBsum - A major Internet resource for protein structural information (EMBL-EBI).
PDBWiki - A community annotated knowledge base of biological molecular structures.
PISA (PDBePISA) - Protein Interfaces, Surfaces and Assemblies tool, and prediction of probable quaternary structures (EMBL-EBI).
PRINTS - A compendium of protein fingerprints, a group of conserved motifs used to characterise a protein family.
Motif Scan - ProSite profile and pattern motifs, and Pfam protein families (SIB - ISREC).
PROSITE database of protein domains, families and functional sites (ExPASy - SIB).
Protein Data Bank (PDB) - From the Research Collaboratory for Structural Bioinformatics (RCSB).
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).
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).
Ramachandran plot - Server displaying main chain torsion angles from an input protein of known structure (Supercomputer Education and Research Centre, Bangalore).
SALIGN - A multiple protein sequence/structure alignment server based on use of MODELLER (see previous section) (Sali Lab, University of California, San Francisco).
SWISS-MODEL Repository - Database of annotated 3-D comparative protein structure models generated by the ExPASy modelling pipeline SWISS-MODEL (see preceding section).
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

CATH Protein Structure Classification Database  - Searchable database of protein structures in PDB classified by domain structure and superfamily (Orengo Group, University College, London).
Combinatorial Extension (CE) Facility for comparing and aligning protein structures (RCSB PDB).
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).
FATCAT - Flexible structure AlignmenT by Chaining Aligned fragment pairs allowing Twists (Sanford-Burnham Medical Research Institute, US).
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).
PASS2 - Protein Alignments organised as Structural Superfamilies (National Centre for Biological Sciences (NCBS), Bangalore, India).
PDBeFold Secondary Structure Matching (SSM) service for the interactive comparison, alignment and superposition of protein structures in 3-D (EMBL-EBI).
PeCoP - Server that looks for Persistently Conserved Positions in sequences of close and distant protein family members.
Pfam -  Protein families database of alignments and hidden Markov models (EMBL-EBI).
POSA (Partial Order Structure Alignment). Multiple flexible structure alignment using partial order graphs.
ProDom - Protein domain families database automatically generated from the UniProt Knowledge Database.
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).
SMART (Simple Molecular Architecture Research Tool) - Protein domain database and sequence analysis facility (EMBL).
TOPSCAN A rapid method for comparing protein structures based on their secondary structures (University College London, UK).
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

PSORT - Prediction of protein sorting signals and localization sites in amino acid sequences.
SignalP - Prediction of signal peptide cleavage sites in protein sequences (Center for Biological Sequence Analysis, (CBS), Technical University of Denmark).
SOSUIsignal Signal peptide prediction server (Department of Biotechnology, Tokyo University of Agriculture and Technology).
TargetP - Predicts subcellular location of eukaryotic proteins (Center for Biological Sequence Analysis, (CBS), Technical University of Denmark).

Membrane proteins and topology prediction

DAS - DAS (Dense Alignment Surface method) Transmembrane prediction server (Stockholm Bioinformatics Center).
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).
Membrane Protein Resources (Stephen White laboratory, University of California, Irvine).
Membrane Proteins of Known 3D Structure - continuously updated list from the Stephen White laboratory, University of California, Irvine.
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).
orienTM - Predicts orientation (topology) of transmembrane proteins from sequence (hosted by University of Athens).
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).
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).
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).
Myosin Home Page (MRC Laboratory of Molecular Biology, Cambridge, UK).
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).
PPAR Resource Page - Information site for the Peroxisome Proliferator-Activated Receptors (Penn State University, US).
Protein Kinase Resource (PKR)
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

ABRF list of commercial protein analysis facilities (The Association of Biomolecular Resource 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)
Database of Interacting Proteins (DIP; University of California).

Delta Mass Database of Protein Post Translational Modifications (ABRF).

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.
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).
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).
BioInformatics and Molecular Analysis Section (BIMAS) - Center for Information Technology (CIT), NIH.
Bioinformatics.ca (Canadian bioinformatics portal).
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.
Institute of Bioinformatics and Biotechnology (IBB) - University of Pune, India).
International Society for Computational Biology (ISCB).
Mathematical, Computational and Systems Biology (MCSB; University of California, Irvine).
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).
The Open Bioinformatics Foundation (O|B|F) - non-profit, volunteer-run organisation focused on supporting open-source programming in bioinformatics.

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This page was last updated:
Monday October 23, 2017

 

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