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Henriette L. Capel, Odysseas Vavourakis, Benjamin H. Williams, Christopher R. Taylor, and Charlotte M. Deane
The Structural Antibody DatabaseThe Structural Antibody Database (SAbDab) [1] is a publicly available repository of experimentally determined antibody structures, first released in 2013. Explicit support for single-domain antibo...
For the last few months, I’ve been building an agent around OPIG’s antibody analysis and design tools, and I thought I’d share some practical notes from the process.
An agent is a language model that doesn’t just answer questions but can also decide what to do, call tools, and follow workflows. I’m using Claude in these notes, but most of the ideas apply equally wel...
My DPhil uses network representations of protein complexes to predict drug targets, so when a summer school on complex networks came up, I wanted to see what tools and ideas from the broader field I might be missing. The Lake Como School on Complex Networks brought together students an...
In this post I’ll walk through how to set up the CCDC Python API and use the CSD Geometry Analyser to evaluate the geometric quality of molecules from three representative structure-based de novo design models. I’ve put together a small GitHub repo with the full analysis code where we look at bond lengths, angles, torsions, and ring conformations across the three met...