Publications

2025

  1. boltzgen.jpeg
    BoltzGen: Toward Universal Binder Design
    Hannes Stark, Felix Faltings*, MinGyu Choi*, Yuxin Xie*, Eunsu Hur*, Timothy O’Donnell*, Anton Bushuiev*, Talip Uçar*, and 30 more authors
    Preprint, 2025
    BoltzGen is a generative model for binder design based on Boltz-2
    DOI Blog Code
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    One protein is all you need
    Anton Bushuiev*, Roman Bushuiev*, Olga Pimenova, and 9 more authors
    Preprint, 2025
    ProteinTTT enables customizing protein language models to one protein at a time for enhanced performance on challenging targets
    DOI Code
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    Self-supervised learning of molecular representations from millions of tandem mass spectra using DreaMS
    Roman Bushuiev*, Anton Bushuiev*, Raman Samusevich, and 3 more authors
    Nature Biotechnology, 2025
    DreaMS is the first foundation model for mass spectrometry
    DOI Code Dataset Tutorials Poster NEWS
  4. enzymeexplorer.png
    Structure-enabled enzyme function prediction unveils elusive terpenoid biosynthesis in archaea
    Raman Samusevich, Téo Hebra, Roman Bushuiev, Martin Engst, Jonáš Kulhánek, Anton Bushuiev, and 12 more authors
    Preprint, 2025
    DOI Code
  5. marts-db.png
    MARTS-DB: A Database of Mechanisms And Reactions of Terpene Synthases
    Martin Engst, Martin Brokeš, Tereza Čalounová, Raman Samusevich, Roman Bushuiev, Anton Bushuiev, and 7 more authors
    BMC bioinformatics, 2025
    DOI Dataset
  6. strobel2025evaluation.png
    An evaluation methodology for machine learning-based tandem mass spectra similarity prediction
    Michael Strobel, Alberto Gil-de-la-Fuente, Mohammad Reza Zare Shahneh, Yasin El Abiead, Roman Bushuiev, Anton Bushuiev, and 2 more authors
    BMC bioinformatics, 2025
    DOI

2024

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    Learning to design protein-protein interactions with enhanced generalization
    Anton Bushuiev*, Roman Bushuiev*, Petr Kouba, and 8 more authors
    ICLR, 2024
    PPIRef is the first comprehensive dataset of protein-protein interfaces, enabling to train PPIformer for protein-protein interaction design
    DOI Video Code Dataset Poster NEWS
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    MassSpecGym: A benchmark for the discovery and identification of molecules
    Roman Bushuiev, Anton Bushuiev, Niek F. Jonge, and 27 more authors
    NeurIPS Datasets & Benchmarks (Spotlight paper), 2024
    MassSpecGym is the first comprehensive benchmark for molecular discovery with mass spectrometry
    DOI Video Code Dataset Poster NEWS
  3. ppileakage.png
    Revealing data leakage in protein interaction benchmarks
    Anton Bushuiev*, Roman Bushuiev*, Jiřı́ Sedlář, and 4 more authors
    ICLR GEM workshop, 2024
    Benchmarks for protein-protein interactions are contaminated with data leakage. This can be addressed by using interface similarity for data splitting.
    DOI Poster

2023

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    Machine learning-guided protein engineering
    Petr Kouba*, Pavel Kohout*, Faraneh Haddadi*, and 7 more authors
    ACS catalysis, 2023