Biology subjects

Vavourakis, O.

Publications and source records attributed to Vavourakis, O..

2 recordsLinked to original sources

bioRxiv2026

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 have increased demand for standardised, high-quality structure data. Here, we present SAbDab2, re-engineered for the machine-learning 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 standardised, versioned train/test splits. These will be updated every six months going forward, and are available at https://zenodo.org/records/20083995. SAbDab2 itself is updated weekly and is freely available at https://sabdab2.opig.stats.ox.ac.uk.

bioinformatics↗

bioRxiv2026

Sampling antibody conformational ensembles withABodyBuilder4-STEROIDS

Conformational flexibility is fundamental to the function of many proteins and in the case of antibodies can impact key properties such as affinity and specificity. While it is possible to predict single, static protein structures with high accuracy, predicting conformational ensemble remains challenging. Molecular dynamics simulations suffer from high computational costs, while deep learning methods are yet to achieve the same level of accuracy. Here, we introduce ABB4-STEROIDS a generative structure prediction model that samples conformational ensembles of antibodies. We trained our model on 4.2 million structural frames derived from [~]136,000 coarse-grained and a set of 83 new all-atom antibody MD simulations. We benchmarked our model on reproducing MD ensembles and evaluated the diversity of sampled structures and the covered conformational space against experimental evidence. ABB4-STEROIDS achieves state-of-the-art accuracy, particularly within the experimental benchmarks. The model is openly available and provides a robust resource for large-scale investigations of antibody conformational ensembles.

bioinformatics↗