Tag Archives: SAbDab

SAbBox in 2023: ImmuneBuilder and more!

For several years now, we have distributed the SAbDab database and SAbPred tools as a virtual machine, SAbBox, via Oxford University Innovation. This virtual machine allows a user to utilise the tools and database locally, allowing for high-throughput analysis and keeping confidential data within a local network. Initially distributed under a commercial licence, the platform proved popular and, in 2020, we introduced a free academic licence to enable our academic colleagues to use our tools and database locally.

Following requests from users, in 2021 we released a new version of the platform packaged as a Singularity container. This included all of the features of SAbBox, allowing Linux users to take advantage of the near bare-metal performance of Singularity when running SAbPred tools. Over the past year, we have made lots of improvements to both SAbBox platforms, and have more work planned for the coming year. I’ll briefly outline these developments below.

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CryoEM is now the dominant technique for solving antibody structures

Last year, the Structural Antibody Database (SAbDab) listed a record-breaking 894 new antibody structures, driven in no small part by the continued efforts of the researchers to understand SARS-CoV-2.

Fig. 1: The aggregate growth in antibody structure data (all methods) over time. Taken from http://opig.stats.ox.ac.uk/webapps/newsabdab/sabdab/stats/ on 25th May 2022.

In this blog post I wanted to highlight the major driving force behind this curve – the huge increase in cryo electron microscopy (cryoEM) data – and the implications of this for the field of structure-based antibody informatics.

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