Author Archives: Henriette Capel

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

Henriette L. Capel, Odysseas Vavourakis, Benjamin H. Williams, Christopher R. Taylor, and Charlotte M. Deane

The Structural Antibody Database 

The Structural Antibody Database (SAbDab) [1] 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 [2]. Detailed annotations and consistent maintenance have made SAbDab a central resource supporting important advances in the field. SAbDab has been used to study antibody-antigen interactions, including SARS-CoV-2; to predict antibody structure; to design antibodies de-novo; and to investigate antibody flexibility. 

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Exploring the Protein Data Bank programmatically

The Worldwide Protein Data Bank (wwPDB or just the PDB to its friends) is a key resource for structural biology, providing a single central repository of protein and nucleic acid structure data. Most researchers interact with the PDB either by downloading and parsing individual entries as mmCIF files (or as legacy PDB files), or by downloading aggregated data, such as the RCSB‘s collection in a single FASTA file of all polymer entity sequences. All too often, researchers end up laboriously writing their own file parsers to digest these files. In recent years though, more sophisticated tools have been made available that make it much easier to access only the data that you need.

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