Jonathan Funk

This paper introduces a hybrid quantum-classical pipeline for designing MHC-binding peptides, showing that quantum-derived priors improve the yield of strong binders, especially for understudied HLA alleles.

An all-atom diffusion model using a 14-atom residue representation and sparse U-Net architecture accelerates biomolecular design 10-fold, enabling experimentally validated DNA-binding proteins and multi-turnover cysteine hydrolases.

AtomWorks, a modular atom-level data framework, trains structure prediction and design models; the resulting RF3 improves chirality handling and performs between AF3 and Boltz.

ProteusAI is an open-source platform that streamlines ML-guided protein design and engineering, improving proteins and enzymes efficiently within the DBTL cycle.