ABodyBuilder3: improved and scalable antibody structure predictions

Abstract

SUMMARY: In this article, we introduce ABodyBuilder3, an improved and scalable antibody structure prediction model based on ABodyBuilder2. We achieve a new state-of-the-art accuracy in the modelling of CDR loops by leveraging language model embeddings, and show how predicted structures can be further improved through careful relaxation strategies. Finally, we incorporate a predicted Local Distance Difference Test into the model output to allow for a more accurate estimation of uncertainties. AVAILABILITY AND IMPLEMENTATION: The software package is available at https://github.com/Exscientia/ABodyBuilder3 with model weights and data at https://zenodo.org/records/11354577.