The ABCD database: a repository for chemically defined antibodies

Abstract

The ABCD (for AntiBodies Chemically Defined) database is a repository of sequenced antibodies, integrating curated information about the antibody and its antigen with cross-links to standardized databases of chemical and protein entities. It is freely available to the academic community, accessible through the ExPASy server (https://web.expasy.org/abcd/). The ABCD database aims at helping to improve reproducibility in academic research by providing a unique, unambiguous identifier associated to each antibody sequence. It also allows to determine rapidly if a sequenced antibody is available for a given antigen.

A recombinant antibody toolbox for Dictyostelium discoideum

“…We hope that these efforts will facilitate work and increase reproducibility in this scientific community. We further hope that it will encourage others to take part in this common enterprise by (i) sequencing their own hybridomas and depositing the sequences in the ABCD database (https ://web.expas y.org/abcd/; [47]); (ii) selecting and characterizing antibodies to new Dictyostelium proteins; and (iii) publishing the results obtained with these antibodies.…”

“…To characterize the converted rAbs, immunofluorescence and/or western blot experiments were performed, comparing the original IgG produced by the hybridoma Table 1 List of sequenced hybridomas; highlighted in bolditalic, the antibodies converted to rAbs a ABCD nomenclature (https ://web.expas y.org/abcd/); the ABCD database is a manually curated repository of sequenced antibodies [47] b "Original references" correspond to the first descriptions of a monoclonal antibody. "rAb references" describe the characterization of the converted rAbs c The recombinant versions of these antibodies were not produced efficiently in our hands In (b), the converted rAb has a mouse Fc, and double immunolabelling could not be performed; staining patterns are identical.…”

AF291 and AE391 antibodies recognize a Dictyostelium HA-tagged protein by Western blot

“…Antibodies: ABCD_AF291 and ABCD_AE391 (ABCD nomenclature, web.expasy.org/abcd/; Lima et al, 2019) were produced by the Geneva Antibody Facility (www.unige.ch/antibodies/) as mini-antibodies with the antigen-binding scFv fused to the Fc region of a mouse IgG (IgG2b for AF291 and IgG2a for AE391). The synthesized scFv sequences (GeneArt, Invitrogen) correspond to the sequences of the variable regions of the monoclonal anti-HA clones 12CA5 (for AF291, Niman et al, 1983) and 26/9 (for AE391, Churchill et al, 1994) joined by a peptide linker (GGGGS) 3 .…”

AI239, RB94 and RB95 antibodies recognize the Glutathione S-transferase protein by ELISA

“…ABCD_RB094, ABCD_RB095, ABCD_AI239, ABCD_AF209 and ABCD_AF212 antibodies (ABCD nomenclature, https://web.expasy.org/ abcd/; Lima et al, 2019) were produced by the Geneva Antibody Facility (www.unige.ch/medecine/antibodies/) as mini-antibodies with the antigen-binding scFv fused to a mouse IgG2A Fc. The synthesized scFv sequences (GeneArt, Invitrogen) for AI239, AF209 and AF212 correspond to the sequences of the variable regions of the VHH, VHii and VHG64 clones (Lin et al, 2018;O'Brien et al, 1999) joined by a peptide linker (GGGGS) 3 .…”