Douglas L. Theobald

This paper investigates the evolutionary tradeoff between enzyme activity and resistance to mycophenolic acid (MPA) and finds that resistance correlates with reduced catalytic efficiency across both ancestral and extant enzymes.

GTRspmix improves protein phylogenetics by incorporating multiple exchangeability matrices into mixture models, enhancing fit and reducing long-branch attraction artifacts.

This study compares the evolvability of an ancestrally reconstructed and modern adenylate kinase, finding that the ancestral enzyme tolerates more mutations and generates more viable variants.

The paper solves the crystal structure of caryolan-1-ol synthase with and without a substrate analog, revealing structural changes that suggest a mechanism for anti-Markovnikov cyclization.

This paper introduces THESEUS-PP, a probabilistic programming approach for protein structure superposition that uses Bayesian models to account for correlated atom positions and heteroscedasticity.