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Novel Computational Protein Design Algorithms with Sparse Residue Interaction Graphs, Ensembles, and Mathematical Guarantees, and their Application to Antibody Design

Ph. D. Defense
Speaker Name
Jonathan Dragon Jou
Date and Time

Computational structure-based protein design seeks to harness the incredible biological power of proteins by designing proteins with new structures and even new function. In this dissertation, we present new algorithms to more efficiently search over two models of protein design: design with sparse residue interaction graphs, and design with conformational ensembles. These algorithms build upon existing provable algorithms: they retain all mathematical guarantees of preceding provable methods while providing both efficiency gains and novel theoretical results.