PhD Dissertation Defense: Christian Choe

Title: RNA Calculators and Protein Sculpting
Abstract: The talk will consist of two parts.
RNA Calculators:
Using crowdsourced RNA designs from the online game Eterna, we demonstrate compact single-molecule sensors for tasks ranging from single input sensors to a complex three-input tuberculosis diagnostic. Inspired by player strategies, we developed Nucleologic, a Monte Carlo tree search algorithm, enabling automated design of similarly sophisticated nucleic acid sensors.
Protein Sculpting:
Designing de novo binding proteins for arbitrary epitopes remains an open challenge, especially using antibody-like folds that rely on flexible loops in their binding interface. We present Sculptor, a deep generative design algorithm that creates epitope-specific binders by jointly optimizing protein structure with a rotamer interaction field to engage the user chosen epitope. We have used Sculptor to design monobodies and nanobodies for a variety of targets ranging from three-finger toxin to plasmodium lactate dehydrogenase.
Please contact Madelyn Bernstein for the Zoom link