Woody Ahern

This paper develops a computational method to design glycoproteins with controlled N-linked glycan composition by encoding glycan location and structure into amino acid sequences.

RFdiffusion2 scaffolds unindexed atom-level catalytic active sites via flow matching without inverse rotamer enumeration, solving all 41 in silico benchmark cases and yielding active de novo enzymes across four reactions.

This paper designs highly active metallohydrolases using a new generative AI method, achieving kcat/KM values up to 53,000 M-1 s-1 without experimental optimization.

This paper introduces RFD2-MI, a deep learning framework for designing phosphotyrosine peptide binders, showing high specificity and affinity for phosphorylated targets.

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.

This study designs novel serine hydrolases with high catalytic efficiency using computational methods, achieving structures close to design models and distinct from natural enzymes.

This paper introduces RFAA and RFdiffusionAA, models that can predict and design complex biomolecular assemblies including proteins, nucleic acids, small molecules, and covalent modifications.

Fine-tuning RoseTTAFold as a diffusion denoiser gives RFdiffusion, a general protein backbone generator; a designed influenza haemagglutinin binder matched its model by cryo-EM.

Millstone is a web-based platform for microbial genome analysis and engineering that automates genotype comparison and visualization for projects with up to hundreds of genomic samples.