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Peer-reviewedCC BY 4.0Nucleic Acids Research

OpenAntigens: a structure-aware database for antigen construct design across the human cell-surface and secreted proteome

  • Andre A R Teixeira1
  • Haisun Zhu1
  • Deepash Kothiwal1
  • Ruili Cao1
  • Allan Mills1
  1. 1Institute for Protein Innovation , Boston, MA 02115 ,
Open at sourcePDFDOICite

Abstract

Choosing which region of a protein to express remains poorly standardized in antibody discovery, recombinant reagent generation, structural biology, and computational binder design. For human cell-surface and secreted proteins, this requires reconciling topology, processing, predicted, and experimental structure, modifications, interaction partners, orthologs, paralogs, and cross-reactivity risk before ordering DNA. OpenAntigens is a free, no-login database of construct-design reports for 5328 human secreted, GPI-anchored, single-pass, and multipass proteins. It integrates UniProt topology, AlphaFold pLDDT and PAE, PDB precedent, InterPro and Pfam domains, mouse and cynomolgus orthologs, paralog and family context, Open Targets disease associations, partner and assembly context, and BLAST searches. It provides 55 305 construct suggestions spanning full design regions, PDB-backed boundaries, annotated domains, pLDDT/PAE-derived regions, and membrane-expression options, plus 148 722 sequence-similarity hits to help choose constructs and assess cross-reactivity. For targets with compatible AlphaFold models, the interactive designer links sequence, structure, pLDDT, and PAE, allowing users to revise boundaries and export species-equivalent sequences with real-time cysteine and modification warnings. OpenAntigens places reproducible construct suggestions, comparative context, and browser editing in one workflow, reducing manual reconciliation across resources. OpenAntigens is available at openantigens.org.

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Cite

BibTeXRIS
BibTeX
@article{teixeira2026openantigens,
  title = {{OpenAntigens: a structure-aware database for antigen construct design across the human cell-surface and secreted proteome}},
  author = {Andre A R Teixeira and Haisun Zhu and Deepash Kothiwal and Ruili Cao and Allan Mills},
  journal = {Nucleic Acids Research},
  year = {2026},
  month = oct,
  doi = {10.1093/nar/gkag1051},
  url = {https://academic.oup.com/nar/advance-article/doi/10.1093/nar/gkag1051/9004253},
  note = {CC BY 4.0},
}
RIS
TY  - JOUR
TI  - OpenAntigens: a structure-aware database for antigen construct design across the human cell-surface and secreted proteome
AU  - Andre A R Teixeira
AU  - Haisun Zhu
AU  - Deepash Kothiwal
AU  - Ruili Cao
AU  - Allan Mills
PY  - 2026
DA  - 2026/10/29
JO  - Nucleic Acids Research
DO  - 10.1093/nar/gkag1051
UR  - https://academic.oup.com/nar/advance-article/doi/10.1093/nar/gkag1051/9004253
AB  - Choosing which region of a protein to express remains poorly standardized in antibody discovery, recombinant reagent generation, structural biology, and computational binder design. For human cell-surface and secreted proteins, this requires reconciling topology, processing, predicted, and experimental structure, modifications, interaction partners, orthologs, paralogs, and cross-reactivity risk before ordering DNA. OpenAntigens is a free, no-login database of construct-design reports for 5328 human secreted, GPI-anchored, single-pass, and multipass proteins. It integrates UniProt topology, AlphaFold pLDDT and PAE, PDB precedent, InterPro and Pfam domains, mouse and cynomolgus orthologs, paralog and family context, Open Targets disease associations, partner and assembly context, and BLAST searches. It provides 55 305 construct suggestions spanning full design regions, PDB-backed boundaries, annotated domains, pLDDT/PAE-derived regions, and membrane-expression options, plus 148 722 sequence-similarity hits to help choose constructs and assess cross-reactivity. For targets with compatible AlphaFold models, the interactive designer links sequence, structure, pLDDT, and PAE, allowing users to revise boundaries and export species-equivalent sequences with real-time cysteine and modification warnings. OpenAntigens places reproducible construct suggestions, comparative context, and browser editing in one workflow, reducing manual reconciliation across resources. OpenAntigens is available at openantigens.org.
SN  - 0305-1048
SN  - 1362-4962
ER  -