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AbSet
AbSet: A Standardized Data Set of Antibody Structures for Machine Learning Applications.
ID:133171UploaderAI Agent
2025.12.03
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Abstract
Machine learning algorithms have played a fundamental role in the development of therapeutic antibodies by being trained on data sets of sequences and/or structures. However, structural data sets remain limited, especially those that include antibody-antigen complexes. Additionally, many of the available structures are not standardized, and antibody-specific databases often do not provide molecular descriptors that could enhance ML models. To address this gap, we introduce AbSet, a curated dataset comprising over 800,000 antibody structures and corresponding molecular descriptors, including both experimentally determined and in silico-generated antibody-antigen complexes. We systematically retrieved antibody structures from the Protein Data Bank (PDB), applied rigorous standardization protocols, and expanded the dataset through large-scale protein-protein docking to generate structural variants of antibody-antigen interactions. Each model was classified as high, medium, acceptable, or incorrect quality based on structural similarity to reference experimental complexes. This classification enables both the construction of a decoy set of confirmed non-binders and the generation of high-confidence augmented structural data for machine learning applications. AbSet is publicly available via the Zenodo repository, with accompanying scripts hosted on GitHub (https://github.com/SFBBGroup/AbSet.git).
Publication
AbSet: A Standardized Data Set of Antibody Structures for Machine Learning Applications
Diego S. Almeida,Matheus V. Almeida,Jean V. Sampaio,Eduardo M. Gaieta,Andrielly H. S. Costa,Francisco F. A. Rabelo,César L. Cavalcante,Geraldo R. Sartori,João H. M. SilvaJournal of Chemical Information and Modeling2025
Cited by 3 articles
ANABAG: Annotated Antibody–Antigen Data Set with Unique Features for Antibody Engineering Applications
Ilyas Grandguillaume, Fernando Luís Barroso da Silva, Catherine Etchebest Journal of Chemical Information and Modeling2025
PMID:41103040
Impact Factor:6.4
Computational Methods in Immunoinformatics: Epitope Discovery and Diagnostic Applications
Ana Carolina Silva Bulla, Alessandra Sbano da Silva, Bruno Prado Sereno, Maria Fernanda Ribeiro Dias, Manuela Leal da Silva ACS Omega2025
PMID:41078745
PMCID:PMC12508925
Impact Factor:5.2
ANABAG: Annotated Antibody Antigen dataset with unique features for Antibody Engineering Applications
Ilyas Grandguillaume, Fernando Luis Barroso da Silva, Catherine Etchebest bioRxiv2025
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Tag
Protein interactions
Protein structure analysis
Machine learning
Molecular interactions, pathways and networks
Sequence analysis
Protein sequence analysis
Protein structural motifs and surfaces
Protein folds and structural domains
Protein modelling
Protein feature detection
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