OpenAntigens code
The OpenAntigens software is released under the Apache License 2.0. This includes the portal renderer, command-line tools, data-retrieval code, analysis logic, and supporting scripts unless a specific file states otherwise.
Structure-aware antigen database
Use conditions
Terms for OpenAntigens data and software
OpenAntigens is a research database and construct-design portal built from public biological resources plus OpenAntigens-generated computational annotations. These terms separate the OpenAntigens software, generated annotations, and third-party source data.
Summary
| Material | Terms | Notes |
|---|---|---|
| OpenAntigens software | Apache License 2.0 | Applies to the project source code unless a file states otherwise. |
| OpenAntigens-generated annotations | CC BY 4.0 | Applies to OpenAntigens-created construct recommendations, classifications, computed summaries, derived report text, portal index metadata, and related derived annotations. It does not cover AlphaFold 3 fallback structures or files derived from them (see the AlphaFold 3 row below). |
| Third-party source data | Original source terms apply | Sequences, structures, identifiers, disease associations, literature counts, and source annotations retain the terms, licenses, and citation expectations of the databases from which they were obtained. |
These terms describe research-data reuse for this release. Legal review and source-database compliance remain the responsibility of the person or organization reusing the data.
OpenAntigens annotations
OpenAntigens-generated annotations are released under Creative Commons Attribution 4.0 International (CC BY 4.0). Reusers may share and adapt these annotations, including for commercial use, provided appropriate attribution is given.
This CC BY 4.0 grant excludes AlphaFold 3 fallback structures and any files derived from them. Those structures are provided for non-commercial use only and remain governed by the AlphaFold Server Output Terms of Use; each report that uses such a model shows an on-page notice.
Third-party source data
OpenAntigens reports may include or derive from third-party identifiers, protein sequences, AlphaFold structures and confidence metrics, PDB mappings, domain annotations, disease associations, literature counts, BLAST databases, and source links. Those materials retain the terms and citation requirements of their original providers.
Research use
OpenAntigens is a research-use computational resource. Diagnosis, clinical decision-making, regulatory submissions, therapeutic selection, manufacturability claims, and expression-performance claims require independent expert review and experimental validation.
Source database terms and attribution
The table summarizes major sources used by OpenAntigens. Official source terms control reuse requirements.
| Source | Used for | License / terms summary | Link |
|---|---|---|---|
| UniProt | Reviewed protein records, sequences, features, topology, domains, PTMs, entry names | Copyrightable database content is under CC BY 4.0; attribution required. | UniProt license |
| AlphaFold DB | Predicted structures, pLDDT, PAE, structure visualizations | Data are available under CC BY 4.0; AlphaFold predictions are theoretical models and provided as-is. | AlphaFold DB |
| AlphaFold 3 artifacts | Local predicted structures and confidence values accepted only after sequence validation | AlphaFold Server Output Terms apply. The outputs are available for non-commercial use and carry restrictions on redistribution, docking or screening use, and training related biomolecular structure-prediction technology. Public release requires clear notice of the AlphaFold Server Output Terms and any modifications. | AlphaFold Server Output Terms |
| RCSB PDB / wwPDB | Experimental structure evidence and construct-boundary precedent | PDB archive and RCSB API data are available under CC0 1.0; attribution to original structure authors is encouraged. | RCSB usage policy |
| GPCRdb | GPCR class/family annotations, segment boundaries, generic residue numbering, conserved motif context, and GPCR-focused interpretation | GPCRdb source-specific terms and citation expectations apply. Cite the main GPCRdb reference and any page-specific GPCRdb references relevant to reused annotations. | GPCRdb citing GPCRdb web services |
| Open Targets Platform | Indirect and direct target-disease association scores, disease links, and disease-aware search | Platform data are marked CC0 1.0; citation of Open Targets is expected in accordance with good scientific practice. | Open Targets licence |
| NCBI RefSeq / NCBI Protein / NCBI Gene | Ortholog protein accessions and sequences in RefSeq-backed reference tables, including mouse and cynomolgus fallback/provenance records | NCBI places no restrictions on molecular data but cannot transfer rights that may belong to submitters or third parties; acknowledge NCBI/NLM where appropriate. | NCBI policies |
| InterPro, Pfam, EMBL-EBI resources | Domain/family annotations and family context | EMBL-EBI expects attribution and may apply source-specific terms; Pfam is CC0. | EMBL-EBI terms |
| HGNC and Ensembl | Human gene symbols, family/paralog context, gene links | Source-specific terms and attribution expectations apply. | HGNC Ensembl |
| PubTator3 / PubMed | Literature-hit counts and literature links | NCBI/NLM policies apply; article text and abstracts may have separate copyright conditions. | PubTator3 |
| CiteAb | External antibody-search link for each target | CiteAb catalog content stays external to OpenAntigens downloads and reports. | CiteAb |
Download scope
OpenAntigens downloads contain derived annotations alongside source-derived fields such as accessions, sequences, structure-confidence values, BLAST hit descriptions, disease associations, and links. Original source terms remain attached to source-derived fields included in an OpenAntigens file.
Attribution
Recommended attribution: OpenAntigens, Institute for Protein Innovation, created by Andre A. R. Teixeira. For publications or redistributed datasets, include the portal build date, downloaded artifact name, OpenAntigens version when available, and the relevant source databases.
Endorsement
References or links to third-party databases, products, antibodies, structures, publications, or disease associations identify source material and external resources. They carry no endorsement by OpenAntigens, the Institute for Protein Innovation, the source database providers, or any listed institution.
Warranty
OpenAntigens is provided as-is and without warranties of accuracy, completeness, non-infringement, merchantability, fitness for a particular purpose, expression performance, antigenicity, developability, or suitability for any specific use.
Limitations and user responsibility
Construct recommendations, cross-reactivity rankings, paralog/family matrices, disease associations, pLDDT/PAE interpretation, and cysteine/furin warnings are computational annotations. Independent review, experimental validation, biosafety review, intellectual-property review, and compliance with institutional, funder, journal, clinical, regulatory, and commercial requirements remain the responsibility of the person or organization using the data.
OpenAntigens data may be incomplete, stale, or affected by source-database updates, sequence-version changes, isoform differences, species-specific annotation gaps, alignment errors, structure-model uncertainty, and BLAST database composition.
Corrections, licensing questions, and takedown requests
Responsible creator and contact: Andre A. R. Teixeira, Institute for Protein Innovation, andre.teixeira@proteininnovation.org.
Contact us to report incorrect attribution, problematic redistribution of source data, stale or incorrect annotations, broken links, or data requiring correction or removal.