Viet Vu is a rising senior undergraduate student at Harvard University studying Computational Biology and is currently participating in this summer’s Rosetta Commons Research Experience for Undergraduates program, which is supported by the National Science Foundation.
Viet will work alongside Nick Randolph, a rising third year graduate student in the Kuhlman lab and an NSF Graduate Research Fellow, who has a background in Applied Mathematics and Chemical Engineering.
This summer Viet and Nick will work together over 8 weeks to create a deep learning-based model that predicts metal binding sites. Metal binding sites are common within proteins, with roughly a third of all protein structures in the Protein Data Bank containing a metal ion. These sites are crucial for a variety of functions, including notably catalysis and transition state stabilization. While traditional physics-based methods have had some success in the design of metal binding sites, design of these sites is often time-consuming. Nick and Viet aim to develop a deep learning-based model that, given a protein scaffold, will identify sets of residues that can be mutated to create a favorable metal binding site.
Additionally, as a Rosetta REU intern, Viet spent one week in a Rosetta Code School that covered topics such as PyRosetta and community coding prior to joining the Kuhlman Lab to conduct research. To end the summer internship, Viet and other Kuhlman Lab members will travel to Seattle and Leavenworth, Washington to present their work at the annual RosettaCON conference held from August 9th to 12th.