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

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. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=81 SRC="FIGDIR/small/741735v1_ufig1.gif" ALT="Figure 1"> View larger version (28K): org.highwire.dtl.DTLVardef@11171e4org.highwire.dtl.DTLVardef@4c41b8org.highwire.dtl.DTLVardef@6ebf30org.highwire.dtl.DTLVardef@ca21fa_HPS_FORMAT_FIGEXP M_FIG C_FIG