NAStructuralDB : Structural database to facilitate computational studies of molecular modeling and recognition of proteins with special focus on antibody-antigen interactions
Open accessPreprint — published as 10.1080/19420862.2026.2630438 · Paper page
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® 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®, 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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SAbDab2: The structural antibody database in the age of machine learningPreprint
Capel, H., Vavourakis, O., Williams, B. H., Taylor, C. R., & Deane, C. M. (2026) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.64898/2026.06.16.732554 · Cited by 3 · see citing works
ASD: Antigen-Specific Antibody Database
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“GenBank , Literature, Patents, and Structures 43 databases were all obtained from internal NaturalAntibody resources.”
Self-citationKrawczyk, K., Dudzic, P., & Kumar, S. (2026) · bioRxiv · doi:10.64898/2026.09.08.750039
“To test the fidelity of our re-implementation, we constructed structure and sequence datasets sampled from the non-redundant antibody, nanobody and protein-complex sets of the NA Structural Database (Chomicz et al. 2026).”
Self-citationRePaRank: An Efficient Architecture for Antibody-Antigen Interface Prediction by Proximity RankingPreprint
Bednarek, J., Janusz, B., & Krawczyk, K. (2026) · bioRxiv · doi:10.64898/2026.03.03.708462
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Self-citationASD: antigen-specific antibody database
Czerwiński, A., Dudzic, P., Wójtowicz, K., et al. (2026) · mAbs · doi:10.1080/19420862.2026.2623330
Self-citation
- Authors
- Chomicz, D., Dudzic, P., Wrobel, S., Gawłowski, T., Demharter, S., Spreafico, R., Minoux, H., Phillips, A., & Krawczyk, K.
- Affiliations
- Wrocław University of Science and Technology (PL)
- Genmab (United States) (US)
- Sanofi (France) (FR)
- Corresponding author
- Krawczyk, Konrad
- ORCID
- Venue
- mAbs
- Publisher
- openRxiv
- Published
- 2025-10-17
- Volume
- 18
- Issue
- 1
- Pages
- 2630438-2630438
- ISSN
- 1942-0862 (ISSN-L)
- OpenAlex
- W7134287346
- Cited by
- 4
- References
- 38
- Citations by year
- 2026: 4
- FWCI
- 8.27
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Licence
- Locations
- mAbs (publishedVersion, cc-by-nc)
- bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion, cc-by)
- PubMed (publishedVersion)
- PubMed Central (publishedVersion, cc-by-nc)
- DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › vaccines and immunoinformatics approaches
- Health Sciences › Medicine › Radiology, Nuclear Medicine and Imaging › Monoclonal and Polyclonal Antibodies Research
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Protein Structure and Dynamics
- Keywords
- antigen-antibody reaction, nanobodies, VHH, protein-protein contacts, epitope prediction, antibody binding sites, surface accessibility, biologic therapeutics, protein-protein interaction prediction
- MeSH terms
- Antigen-Antibody Reactions, Epitopes, Antigens, Humans, Models, Molecular, Protein Conformation, Computational Biology, Databases, Protein, Single-Domain Antibodies
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