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.

Figure 1.

Examples of antibody entries. Each entry has a unique identifier with the format ABCD_[A-Z][A-Z][0–9][0–9][0–9]. The Antibody table contains names and synonyms of the antibody, a published reference (with a link to PubMed, in case of scientific papers, or to the WIPO database, in case of a patent), and technical applications. The antibody sequence (see Figure 2 legend) is available on the Cross-references and Publications links provided, or upon request. (A) Target is a Protein: the Antigen table contains the name and species of target, a link to the UniProtKB UID, and information on the epitope when available. (B) Target is a Chemical: the Antigen table contains the target name, a link to the ChEBI UID, and information on the epitope when available.

Figure 2.

Antibody sequence information. (A) An immunoglobulin consists of constant (C, in gray) and variable (V, in blue and green) chains. The paratope (or specific binding site) of an antibody is located at the variable moiety of the light (V_L) and heavy (V_H) chains. (B) The ABCD database stores as sequence information the amino-acid sequence of both V_L and V_H chains (the example given corresponds to sequence of entry ABCD_AI179, the anti-cMyc 9E10 clone).