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bioRxiv · 10.1101/2025.02.25.640196

Fast, accurate parsing of antibody structures and antibody-antigen interactions enables a comprehensive structural antibody database

Huang, X.·Zhou, J.·Chen, S.·Xia, X.·Chen, Y. E.·Xu, J.
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Abstract

Antibody (Ab) structures and antibody-antigen interactions (AAIs) are essential for understanding immune recognition and designing Ab therapeutics. While existing structural Ab databases provide valuable insights, they still have notable limitations. Here, we present SAAINT-parser, an computational workflow for rapid, accurate, and robust extraction of Ab and AAI information from the Protein Data Bank (PDB). SAAINT-parser features precise detection of Ab chains, accurate pairing of Ab chains, and reliable identification of AAIs. The resulting SAAINT-DB contains 18,031 data entries from 9,373 PDB structures, offering a comprehensive and up-to-date resource. Detailed analyses of SAAINT-DB reveals its advantages over the most widely used SAbDab database, particularly in terms of data accuracy and completeness. Furthermore, SAAINT-DB provides nearly twice as many nonredundant, manually curated Ab-Ag binding affinity data compared to SAbDab. Both SAAINT-parser and SAAINT-DB are available as open-source resources, aimed at advancing Ab-related research and benefiting the broader scientific community.

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Huang, X., Zhou, J., Chen, S., Xia, X., Chen, Y. E., Xu, J.. 2025-03-01. Fast, accurate parsing of antibody structures and antibody-antigen interactions enables a comprehensive structural antibody database. https://doi.org/10.1101/2025.02.25.640196

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