Tommi Jaakkola

Atom level enzyme active site scaffolding using RFdiffusion2

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.

BoltzGen: Toward Universal Binder Design

An all-atom diffusion model unifying biomolecular structure prediction and sequence-structure generation designs experimentally validated nanobodies, mini-proteins, and linear or cyclic peptides across 26 diverse targets.

Boltz-2: Towards Accurate and Efficient Binding Affinity Prediction

Boltz-2 predicts protein–ligand affinity from its co-folded structures, nearing free-energy perturbation accuracy (average Pearson 0.66 on a 4-target FEP+ subset) at over 1000× lower compute.

Boltz-1: Democratizing Biomolecular Interaction Modeling

Open-source Boltz-1 predicts biomolecular complex structures comparably to AlphaFold3 and Chai-1 on CASP15 and recent PDB targets; Boltz-steering lets 97% of test-set poses pass physical checks.

Broadly applicable and accurate protein design by integrating structure prediction networks and diffusion generative models

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.