SAbDab2: the structural antibody database in the age of machine learning

The Structural Antibody Database (SAbDab) is a publicly available repository of experimentally determined antibody structures, first released in 2013. Explicit support for single-domain antibodies was added in 2021, with SAbDab-nano. Recently, increasing interest in antibodies has led to a proliferation of novel antibody formats, while simultaneous advances in machine learning (ML) have increased demand for standardized, high-quality structure data. Here, we present SAbDab2, re-engineered for the ML age. It introduces support for a variety of new formats, and makes it easy to retrieve and compare all known structures of a given antibody. In addition, SAbDab2 provides ready access to ML-grade structures of antibody and antibody-antigen-complexes, with standardized, versioned train/test splits. These will be updated every 6 months going forward and are available at https://zenodo.org/records/20083994. SAbDab2 itself is updated weekly and freely available at https://sabdab2.opig.stats.ox.ac.uk.