Xiaoduan Ye

Learn More
Relationships among amino acids determine stability and function and are also constrained by evolutionary history. We develop a probabilistic hypergraph model of residue relationships that generalizes traditional pairwise contact potentials to account for the statistics of multi-residue interactions. Using this model, we detected non-random associations in(More)
Protein engineering by site-directed recombination seeks to develop proteins with new or improved function, by accumulating multiple mutations from a set of homologous parent proteins. A library of hybrid proteins is created by recombining the parent proteins at specified breakpoint locations; subsequent screening/selection identifies hybrids with desirable(More)
Site-directed mutagenesis affects protein stability in a manner dependent on the local structural environment of the mutated residue; e.g., a hydrophobic to polar substitution would behave differently in the core vs. on the surface of the protein. Thus site-directed mutagenesis followed by stability measurement enables evaluation of and selection among(More)
The study of three-dimensional protein structures produces insights into protein function at the molecular level. Graphs provide a natural representation of protein structures and associated experimental data, and enable the development of graph algorithms to analyze the structures and data. This thesis develops such graph representations and algorithms for(More)
  • 1