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

Nature Computational Science volume 2, pages 845–865 (2022)Cite this article

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A preprint version of the article is available at bioRxiv.

Abstract

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.

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Fig. 1: Pipeline for the high-throughput generation of synthetic 3D antibody–antigen structure datasets suited for diverse ML formalizations.
Fig. 2: The Absolut! dataset reflects granular levels of the biological complexity of antibody–antigen binding.
Fig. 3: Classification of binding and non-binding antibody sequences with ML.
Fig. 4: Transferability of ML method rankings and impact of negative examples for pose classification.
Fig. 5: ML prediction of paratope–epitope pairs involved in antibody–antigen binding.

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Data availability

The Absolut! database is available at https://greifflab.org/Absolut and in the NIRD research data archive113. Source data for Figs. 2–5 is available with this paper.

Code availability

The Absolut! package is freely available at https://github.com/csi-greifflab/Absolut/ and on Zenodo114.

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Acknowledgements

We acknowledge generous support by The Leona M. and Harry B. Helmsley Charitable Trust (#2019PG-T1D011, to V.G.), UiO World-Leading Research Community (to V.G.), UiO:LifeScience Convergence Environment Immunolingo (to V.G., G.K.S. and I.H.H.), EU Horizon 2020 iReceptorplus (#825821) (to V.G.), a Research Council of Norway FRIPRO project (#300740, to V.G.), a Research Council of Norway IKTPLUSS project (#311341, to V.G. and G.K.S.), a Norwegian Cancer Society Grant (#215817, to V.G.), and Stiftelsen Kristian Gerhard Jebsen (K.G. Jebsen Coeliac Disease Research Centre) (to L.S. and G.K.S.). This work was not funded by Marie Skłodowska-Curie Actions while grant writing was supported by the German Arbeitsamt. This work was carried out on Immunohub e-Infrastructure funded by University of Oslo and jointly operated by GreiffLab and SandveLab (the authors) in close collaboration with the University Center for Information Technology, University of Oslo, IT-Department (USIT). We acknowledge T. Malliavin (Institut Pasteur, Paris, France) for comments and suggestions that helped in the analysis of the results, and C. Schneider for helping us reproduce the DLAB-VS pipeline.

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Author notes

  1. These authors contributed equally: Philippe A. Robert, Rahmad Akbar.

Authors and Affiliations

  1. Department of Immunology, University of Oslo and Oslo University Hospital, Oslo, Norway

    Philippe A. Robert, Rahmad Akbar, Robert Frank, Igor Snapkov, Andrei Slabodkin, Maria Chernigovskaya, Eva Smorodina, Puneet Rawat, Brij Bhushan Mehta, Ingvild Frøberg Mathisen, Fridtjof Lund-Johansen & Victor Greiff

  2. Department of Informatics, University of Oslo, Oslo, Norway

    Milena Pavlović, Lonneke Scheffer & Geir Kjetil Sandve

  3. ELLIS Unit Linz and LIT AI Lab, Institute for Machine Learning, Johannes Kepler University Linz, Linz, Austria

    Michael Widrich, Sepp Hochreiter & Günter Klambauer

  4. Department of Linguistics and Scandinavian Studies, University of Oslo, Oslo, Norway

    Mai Ha Vu & Dag Trygve Tryslew Haug

  5. Danish Cancer Society Research Center, Translational Cancer Genomics, Copenhagen, Denmark

    Aurél Prósz

  6. The Novo Nordisk Foundation Center for Biosustainability, Autoflow, DTU Biosustain and IT University of Copenhagen, Copenhagen, Denmark

    Krzysztof Abram

  7. Department of Complex Systems in Physics, Eötvös Loránd University, Budapest, Hungary

    Alex Olar

  8. Institute of Medical Engineering and Medical Informatics, School of Life Sciences, FHNW University of Applied Sciences and Arts Northwestern Switzerland, Muttenz, Switzerland

    Enkelejda Miho

  9. aiNET GmbH, Basel, Switzerland

    Enkelejda Miho

  10. Swiss Institute of Bioinformatics, Lausanne, Switzerland

    Enkelejda Miho

  11. Institute of Advanced Research in Artificial Intelligence (IARAI), Vienna, Austria

    Sepp Hochreiter

  12. Department of Mathematics, University of Oslo, Oslo, Norway

    Ingrid Hobæk Haff

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Contributions

Study conception: P.A.R., V.G.; study design: P.A.R., R.A., E.M., D.T.T.H., F.L.-J., S.H., I.H.H., G.K., G.K.S., V.G.; study implementation: P.A.R., R.A., R.F., M.P., M.W., I.S., A.P., K.A., A.O., A.S., M.C., L.S., I.F.M.; contributed data and analysis tools: E.S., P.R., B.B.M., M.H.V.; performed the analysis: P.A.R., R.A., R.F., I.F.M., K.A., A.O., A.S.; wrote the paper: P.A.R., R.A., R.F., M.P., M.W., I.S., A.S., M.C., L.S., E.S., P.R., B.B.M., M.H.V., I.F.M., G.K.S., V.G.

Corresponding authors

Correspondence to Philippe A. Robert or Victor Greiff.

Ethics declarations

Competing interests

E.M. declares holding shares in aiNET GmbH. V.G. declares advisory board positions in aiNET GmbH, Enpicom B.V, Specifica Inc, Adaptyv Biosystems, EVQLV, Omniscope, Diagonal Therapeutics, and Absci. V.G. is a consultant for Roche/Genentech, immunai, and Proteinea. The other authors declare no competing interests.

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Nature Computational Science thanks Charlotte Deane, Pieter Meysman and the other, anonymous, reviewer(s) for their contribution to the peer review of this work. Primary Handling Editor: Fernando Chirigati, in collaboration with the Nature Computational Science team.

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Supplementary information

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Supplementary Results, Discussion, Figs. 1–24, Algorithms, Tables 1–6 and References.

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Robert, P.A., Akbar, R., Frank, R. et al. Unconstrained generation of synthetic antibody–antigen structures to guide machine learning methodology for antibody specificity prediction. Nat Comput Sci 2, 845–865 (2022). https://doi.org/10.1038/s43588-022-00372-4

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