Our Mission
We design new and optimize existing enzymes using computational and experimental tools. Our goal is to understand the fundamental biophysical bases of enzyme function and use that knowledge to engineer enzymes for biodegradation of pollutants and toxins, catalytic therapeutics, and chemistries beyond what biology has explored.
Read more about our research themes →
Research Themes
Our work spans four interrelated themes:
- Designing enzyme selectivity: engineering proteases for catalytic-drug applications, designing stereodivergent biocatalysts.
- Protein and enzyme stabilization: Developing methods for thermostable and solvent-tolerant biocatalysts using physics-based and AI/ML models.
- Stimulus-responsive enzymes and enzyme assemblies: smart enzymes gated by chemical or optical stimuli, and supramolecular fractal architectures.
- Novel computational design methods: design with unnatural amino acids, custom protein design neural networks and language models, constrained generative diffusion, covalent proteins, and force-field development.
See our research page for details →
Lab News
- March 2026: Jonathan Ash successfully defends his PhD. Congratulations, Dr. Ash! Alyssa Lee (1st year, Quantitative Biomedicine PhD program) joins the lab, jointly supervised with Rohan Maddamsetti. Welcome!
- January 2026: Our paper on the design of generalist cyclopropanases with stereodivergent selectivity is published in Nature Communications. Congratulations Zhuofan, Mary, Xinkun, Thakshila, Jermaine, and the Fasan lab.
- November 2025: Jonathan Ash's preprint on graph attention with structural features for predicting functional protein-interface sequences is posted to bioRxiv. Joint work with the Whitehead lab.
- October 2025: "Constrained Diffusion for Protein Design with Hard Structural Constraints" is accepted at ICLR 2026 and posted to bioRxiv. Congratulations Jacob, Austin, Jingyi, and the Fioretto group.
- November 2024: Priscilla's preprint on synergistic multi-pronged inhibition of α-synuclein aggregation by HtrA1 is posted to bioRxiv. Joint work with the Baum lab.