Unconstrained generation of synthetic antibody–antigen structures to guide machine learning methodology for antibody specificity prediction

Machine learning (ML) is a key technology for accurate prediction of antibody–antigen binding. Two orthogonal problems hinder the application of ML to antibody-specificity prediction and the benchmarking thereof: the lack of a unified ML formalization of immunological antibody-specificity prediction problems and the unavailability of large-scale synthetic datasets to benchmark real-world relevant ML methods and dataset design. Here we developed the Absolut! software suite that enables parameter-based unconstrained generation of synthetic lattice-based three-dimensional antibody–antigen-binding structures with ground-truth access to conformational paratope, epitope and affinity. We formalized common immunological antibody-specificity prediction problems as ML tasks and confirmed that for both sequence- and structure-based tasks, accuracy-based rankings of ML methods trained on experimental data hold for ML methods trained on Absolut!-generated data. The Absolut! framework has the potential to enable real-world relevant development and benchmarking of ML strategies for biotherapeutics design.

Schlagwörter

Machine learning, Deep learning, Antibody, Antigen, Specificity, Epitope, Paratope, Structure, Real-world

Fachgebiet (DDC)

600 - Technik, Medizin, angewandte Wissenschaften

Projekt

Veranstaltung

Startdatum der Ausstellung

Enddatum der Ausstellung

Startdatum der Konferenz

Enddatum der Konferenz

Datum der letzten Prüfung

ISBN

ISSN

2662-8457

Sprache

Englisch

Während FHNW Zugehörigkeit erstellt

Ja

Publikationsstatus

Veröffentlicht

Begutachtung

Peer-Review der ganzen Publikation

Open Access-Status

Closed

Lizenz

Zitation

ROBERT, Philippe A., Rahmad AKBAR, Robert FRANK, Milena PAVLOVIĆ, Michael WIDRICH, Igor SNAPKOV, Andrei SLABODKIN, Maria CHERNIGOVSKAYA, Lonneke SCHEFFER, Eva SMORODINA, Puneet RAWAT, Brij Bhushan MEHTA, Mai Ha VU, Ingvild Frøberg MATHISEN, Aurél PRÓSZ, Krzysztof ABRAM, Alex OLAR, Enkelejda MIHO, Dag Trygve Tryslew HAUG, Fridtjof LUND-JOHANSEN, Sepp HOCHREITER, Ingrid Hobæk HAFF, Günter KLAMBAUER, Geir Kjetil SANDVE und Victor GREIFF, 2022. Unconstrained generation of synthetic antibody–antigen structures to guide machine learning methodology for antibody specificity prediction. Nature Computational Science. 19 Dezember 2022. Bd. 2, S. 845–865. DOI 10.1038/s43588-022-00372-4. Verfügbar unter: https://irf.fhnw.ch/handle/11654/46938

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