Improving Antibody-Antigen Interaction Prediction Through Flexibility with ESMFold

Sara Joubbi, Sara Joubbi, Giuseppe Maccari, Giorgio Ciano, Alessio Micheli, Paolo Milazzo, Duccio Medini

2025

Abstract

Antibodies are essential proteins in the immune system due to their capacity to bind to specific antigens. They also play a critical role in developing vaccines and treatments for infectious diseases. Their complex structure, with variable regions for antigen binding and flexible hinge regions, presents challenges for accurate computational modeling. Recent advancements in deep learning have revolutionized protein structure prediction. Despite these advancements, predicting interactions between antibodies and antigens remains challenging, mainly due to the flexibility of antibodies and the dynamic nature of binding events. This study uses fingerprint-based methodologies that incorporate ESMFold confidence scores as a flexibility feature to model Ab-Ag interactions. Our methodology shows how including flexibility has improved Ab-Ag interactions by 3%, achieving an AUC-ROC of 91%.

Paper Citation

in Harvard Style

Joubbi S., Maccari G., Ciano G., Micheli A., Milazzo P. and Medini D. (2025). Improving Antibody-Antigen Interaction Prediction Through Flexibility with ESMFold. In Proceedings of the 18th International Joint Conference on Biomedical Engineering Systems and Technologies - Volume 1: BIOINFORMATICS; ISBN 978-989-758-731-3, SciTePress, pages 603-610. DOI: 10.5220/0013189500003911

in Bibtex Style

@conference{bioinformatics25,
author={Sara Joubbi and Giuseppe Maccari and Giorgio Ciano and Alessio Micheli and Paolo Milazzo and Duccio Medini},
title={Improving Antibody-Antigen Interaction Prediction Through Flexibility with ESMFold},
booktitle={Proceedings of the 18th International Joint Conference on Biomedical Engineering Systems and Technologies - Volume 1: BIOINFORMATICS},
year={2025},
pages={603-610},
publisher={SciTePress},
organization={INSTICC},
doi={10.5220/0013189500003911},
isbn={978-989-758-731-3},
}

in EndNote Style

TY - CONF

JO - Proceedings of the 18th International Joint Conference on Biomedical Engineering Systems and Technologies - Volume 1: BIOINFORMATICS
TI - Improving Antibody-Antigen Interaction Prediction Through Flexibility with ESMFold
SN - 978-989-758-731-3
AU - Joubbi S.
AU - Maccari G.
AU - Ciano G.
AU - Micheli A.
AU - Milazzo P.
AU - Medini D.
PY - 2025
SP - 603
EP - 610
DO - 10.5220/0013189500003911
PB - SciTePress