Author

T.P. Jenkins

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Open access Sep 2026

Multiobjective VHH discovery through integrated high-throughput screening and AlphaFold3-guided structural prioritization

Finding therapeutic antibodies that bind multiple related targets with high affinity and favorable biophysical properties remains challenging and resource-intensive. For snakebite antivenoms, this challenge is critical as treatments must neutralize toxins across multiple snake species. We developed a pipeline combining...

M. D. Overath, Suthimon Thumtecho, E. Rivera-de-Torre et al. · Science Advances · 0 citations

Open access Sep 2026

De novo designed single-domain antibodies protect against lethal cobra venom neurotoxicity in vivo

Generative protein design can now rapidly produce de novo binders with high affinity and functional activity against a wide range of targets, including lethal snake venom toxins. However, so far most reported successes rely on new-to-nature scaffolds with limited therapeutic precedent. Single-domain antibodies (VHHs) o...

M. D. Overath, Emil V. S. Lundquist, Kasper H. Björnsson et al. · bioRxiv · 0 citations

Open access Sep 2026

Specificity-driven protein binder design with Odin-Multi

Odin-Multi is presented, a binder design framework that optimises a shared binder sequence against several complexes simultaneously, applying attractive objectives to on-targets and repulsive objectives to off-targets, and widens the range of binding behaviours accessible to computational design.

Valentas Brasas, C. R. Christensen, Kasper H. Björnsson et al. · bioRxiv · 0 citations

Open access Sep 2026

Learning from tandem mass spectra at scale with a self-supervised foundation model for proteomics

InstaNovo-FM is presented, a self-supervised foundation model for bottom-up proteomics trained to reconstruct masked regions of tandem mass spectra and establishes a unified representation space for peptide fragmentation spectra, enabling robust transferability across the proteomics ecosystem.

M. Nieuwoudt, Marco Reverenna, Divanisha Patel et al. · bioRxiv · 1 citation · ⚡1

Open access Jul 2026

Hybrid quantum-classical de novo design of MHC-binding peptides

Deep generative models have become a leading approach for designing therapeutic molecules, yet efficiently exploring vast biomolecular sequence spaces remains difficult, particularly for targets with limited training data. The prior distribution that seeds a generative model shapes which regions of sequence space it ex...

E. S. Engdal, Jonathan Funk, O. Bacarreza et al. · bioRxiv · 0 citations