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bioRxiv · 10.1101/2025.10.17.683056

NAStructuralDB : Structural database to facilitate computational studies of molecular modeling and recognition of proteins with special focus on antibody-antigen interactions.

Chomicz, D.·Dudzic, P.·Wrobel, S.·Gawlowski, T.·Demharter, S.·Spreafico, R.·Minoux, H.·Phillips, A.·Krawczyk, K.
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Abstract

Studying the interactions between antibodies and antigens is fundamental to the development of novel therapeutic biologics. Predictions of such interactions start with data collection. Though there exist reliable resources to identify antibody structures in the Protein Data Bank (PDB), such data still requires substantial processing to be usable in predictive tasks. Redundancy in sequences needs to be removed to avoid data leakages between train, test and validation sets. Descriptors such as surface accessibility, secondary structure and antibody region information need to be additionally annotated. Information on inter- and intra-molecular contacts, which is crucial to studying paratope/epitope information, needs to be collected. The specialized immunoglobulin format of Nanobodies(R) requires a separate dataset mirroring that of antibodies, given that their structure contains only a single VHH chain. Because antibody-antigen structures account for a small amount of all protein-protein contacts, having a molecular contact reference from other proteins is also desired. To address these issues, we introduce NAStructuralDB (https://naturalantibody.com/na-structural/), a dataset of processed structures of antibodies, Nanobodies(R), proteins and their complexes with molecular contact information and associated annotations. We use the opportunity of having collected the contact data to provide a reference of binding propensities of different residues across distinct contact types. We anticipate that this dataset will accelerate a broad range of predictive tasks by standardizing common, time-consuming data preparation steps in antibody and protein design.

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Chomicz, D., Dudzic, P., Wrobel, S., Gawlowski, T., Demharter, S., Spreafico, R., Minoux, H., Phillips, A., Krawczyk, K.. 2025-10-17. NAStructuralDB : Structural database to facilitate computational studies of molecular modeling and recognition of proteins with special focus on antibody-antigen interactions.. https://doi.org/10.1101/2025.10.17.683056

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