Welcome to the official repository for AntigenDB, a comprehensive and manually curated database of experimentally validated antigens from pathogenic organisms. This resource is designed to support researchers in vaccine development, immunoinformatics, computational vaccinology, and microbiology.
Web Server: https://webs.iiitd.edu.in/raghava/antigendb/ Zenodo : https://doi.org/10.5281/zenodo.20120520
Ansari, H. R., Flower, D. R., & Raghava, G. P. S. (2010). AntigenDB: an immunoinformatics database of pathogen antigens. Nucleic Acids Research, 38 (Database issue), D847–D853. https://doi.org/10.1093/nar/gkp830
AntigenDB is a specialized, value-added database of experimentally validated antigens derived from pathogenic organisms. Unlike existing epitope-oriented databases (IEDB, MHCBN, AntiJen, BCIPEP), AntigenDB is antigen-centric — it covers all experimentally determined antigens regardless of whether epitope information is known, including the large class of protective antigens for which no epitope has yet been identified.
The database integrates information from:
- Literature (PubMed, ScienceDirect)
- Public repositories (SwissProt, GenBank, PDB, GEO, IEDB, MHCBN, AntiJen, BCIPEP)
- Specialized databases (dbPTM, PhosphoELM, RESID, InterPro, DBSubLoc, PSORTdb, IMGT, SYFPEITHI)
- Over 500 antigen entries (proteins, glycoproteins, and lipoproteins)
- Derived from 44 important pathogenic species
- Crystal structure data available for 290 out of 504 antigens
Major genera represented include: Mycobacterium, Plasmodium, Influenza A virus, Helicobacter, Bacillus, Brucella, Clostridium, Hepatitis, Streptococcus, Yersinia, Vibrio, Staphylococcus, Haemophilus, Candida, Anaplasmia, Neisseria, Borrelia, Chlamydia, Shigella, Listeria, Legionella, Pseudomonas, Treponema, Salmonella, and more.
Each antigen entry is organized into six data tables:
- Primary Table — antigen name/synonyms, type (protein/carbohydrate/lipid), amino acid sequence, source organism (linked to NCBI Taxonomy)
- Structural Information — crystal structure (PDB), surface accessibility (ASAView), homology models (Swiss-Model), secondary structure content (DSSP)
- B-cell Epitope — humoral immune response data, specific B-cell epitopes, antibody information, associated PTMs
- T-cell Epitope — T helper and cytotoxic T cell epitopes, MHC I/II binders (with IC50 values), TAP binders, cleavage site mapping, associated PTMs
- Functional Information — SwissProt/GO functional annotation, subcellular localization (DBSubLoc, PSORTdb), functional sites/domains (InterPro), BLAST similarity to host and pathogenic proteins
- Gene Expression — GenBank nucleotide sequence, codon frequency, codon bias (GCUA), expression profiles (GEO)
Covers seven major PTM types compiled from literature and specialized databases:
- N/O/C/S-Glycosylation
- Phosphorylation
- Amidation
- N-Myristoylation
- Tyrosine Sulfation
- Flavin attachment
- LPL attachment site and other methylation/modification types
- 358 antigens with no currently known epitope information — not covered by any existing epitope database
- ~95 Mycobacterium antigens alone that induce immune responses but have no identified epitope
- Structural data available for 290 of 504 antigens
AntigenDB provides experimentally validated antigen data along with:
- Antigen sequence, structure, and functional annotation
- B-cell and T-cell epitope profiles where available
- Subcellular localization and host/pathogen similarity assessment
- Gene expression and codon usage data
- PTM annotations
- Cross-references to 14+ major biological databases
- Integrated analysis tools for antigen discovery and vaccine candidate evaluation
Search across all antigen fields using AntigenDB entry number, antigen name, SwissProt accession number, or source organism. Results can be filtered by antigen type (protein, carbohydrate, lipid) or specific organism via a drop-down menu. Output fields are user-selectable; results can be exported as a data file.
Select an organism of interest and specify output fields to retrieve all available antigens for that pathogen in a tabular format.
Search a query protein sequence against the AntigenDB antigen database using standalone WWW-BLAST with customizable weight matrix and E-score threshold. Identifies antigens with sequence similarity to novel proteins.
Scans all epitopes in AntigenDB against a user-submitted query protein sequence. Returns start and end positions of experimentally defined epitopes matching the query, with links back to the source antigen entries. Identifies known immunogenic regions in target proteins.
Search whether a specific query epitope sequence is present in known antigens within AntigenDB. Returns antigens containing exact or similar epitope matches.
Allows users to submit newly identified antigens not yet present in AntigenDB. Submitted antigens are validated by the AntigenDB team before inclusion.
AntigenDB is built on a SUN systems T-1000 server running Solaris 10.0. The front-end was developed using HTML; the backend uses PostgreSQL as the relational database management system. All CGI and database interfacing scripts were written in PERL. PERL scripts were also used to automatically extract sequence, structural, functional, and gene expression data from SwissProt, GenBank, PDB, and GEO.
- First antigen-centric immunological database — covers experimentally validated antigens regardless of whether epitope data exists
- Fills a critical gap left by epitope-focused databases (IEDB, MHCBN, AntiJen, BCIPEP), which exclude the large proportion of protective antigens with no known epitopes
- Integrates six distinct data categories per entry (sequence, structure, B-cell epitopes, T-cell epitopes, function, gene expression, PTMs) in a single resource
- Includes host and pathogen similarity information to support autoimmune risk assessment in vaccine design
- Provides gene expression and codon usage data — critical for antigen expression-level assessment
- Covers antigen types beyond proteins (carbohydrates, lipids, glycoproteins, lipoproteins)
- Current version primarily contains protein antigens due to their greater availability in the literature
- Certain antigens may be missing due to the scale of literature coverage required
- Not all pathogenic species are represented — selection prioritized organisms with significant global health impact
- Epitope information is absent for 358 entries (~71% of database); these remain uncharacterized in epitope databases
- Adjuvant and route-of-immunization data are not systematically captured
- Vaccine candidate antigen discovery and prioritization
- Immunoinformatics method development for antigen and epitope prediction
- Identification of conserved or unique antigens across pathogenic species
- Assessment of autoimmune risk (host similarity analysis) for vaccine antigens
- Virulence mechanism research in pathogenic microorganisms
- Expression-guided selection of antigens for subunit vaccine design
Email:- raghava@iiitd.ac.in IIIT DELHI
Bioinformatics Centre, Institute of Microbial Technology Sector 39A, Chandigarh, India raghava@imtech.res.in https://webs.iiitd.edu.in/raghava/antigendb/
The Jenner Institute, University of Oxford High Street, Compton, Berkshire, RG20 7NN, UK (Dr. Darren R. Flower — Jenner Investigator, supported by the Jenner Foundation)
This article is distributed under the Creative Commons Attribution Non-Commercial License (CC BY-NC 2.5 UK) © The Author(s) 2009. Published by Oxford University Press.