Monthly Tutorial: Pranam Chatterjee

Speaker: Pranam Chatterjee

Title:Designing Programmable Biologics with Generative Sequence Models

Location: Amy Gutmann Hall, Room 414 (Penn), and via Zoom (email Annie for link)

Lunch will be provided for in-person attendees at Penn (please bring your own drinks)!

Abstract:

In this talk, I will share how my lab develops discrete generative models to design functional biologics for disease and bioremediation. Our work has centered on language models that de novo design peptides to bind and modulate undruggable targets, with experimental validation across rare neurodegenerative disorders, pediatric cancers, and viral infections. Because therapeutic design depends on clinically-viable properties beyond binding (solubility, half-life, non-toxicity), we have developed discrete diffusion algorithms to generate peptides, proteins, mRNAs, and heavy metal sequestrants that are Pareto-optimal across these properties. We have extended these frameworks to discrete flow matching models that generate isoform-specific, domain- and motif-resolved binders under competing therapeutic objectives, enabling the design of potent inhibitors and CAR T cell ligands. Finally, we have recently pioneered Schrödinger Bridge Matching, a new class of generative models that capture both biological states and the trajectories connecting them, from protein folding to drug-induced cell-state transitions, establishing a unified, programmable framework for molecular modeling and design.

Bio:

Pranam Chatterjee is an Assistant Professor of Bioengineering and Computer and Information Science and the Africk-Lesley Distinguished Scholar of Innovation at the University of Pennsylvania. Having earned his SB, SM, and PhD from MIT, his work focuses on the development of core generative algorithms and experimental platforms to design molecules for therapeutics and bioremediation. Professor Chatterjee has received the NIH MIRA Award, Hartwell Individual Biomedical Research Award, and multiple NIH and foundation grants for his work. He has also co-founded numerous companies, including Gameto, Inc., UbiquiTx, Inc., AtomBioworks, Inc., which translates his research into fertility solutions and disease therapeutics.