Machine Learning in Enzymology

After completing studies for the A.B., A.M., and Ph.D. degrees in chemistry at Harvard University, David W. Christianson joined the faculty of the University of Pennsylvania, where he is currently the Roy and Diana Vagelos Professor in Chemistry and Chemical Biology. At Penn, Christianson’s research focuses on the structural and chemical biology of the zinc-dependent histone deacetylases as well as enzymes of terpene biosynthesis. His research accomplishments have been recognized by several awards, including the Pfizer Award in Enzyme Chemistry and the Repligen Award in Chemistry of Biological Processes from the American Chemical Society, a Guggenheim Fellowship, and the Elizabeth S. and Richard M. Cashin Fellowship from the Radcliffe Institute for Advanced Study at Harvard University. Christianson is also a dedicated classroom teacher, and his accomplishments in this regard have been recognized by the Lindback Award for Distinguished Teaching at Penn and a Rhodes Trust Inspirational Educator Award from Oxford University. Christianson has also held visiting professorships in the Department of Biochemistry at Cambridge University and the Department of Chemistry and Chemical Biology at Harvard University. Christianson has served with Prof. Anna Pyle as Co-Editor-in-Chief of Methods in Enzymology since 2015.Dr. Karen N. Allen works at the Department of Chemistry of the Boston University, the Metcalf Center for Science and Engineering Qiang Cui is a Professor of Chemistry at Boston University and also affiliated with Departments of Physics and Biomedical Engineering. He received B.S. in Chemical Physics from the University of Science and Technology of China in 1993, and Ph. D. in Theoretical Chemistry in 1997 from Emory University under the tutelage of Professor Keiji Morokuma. He conducted postdoctoral research with Professor Martin Karplus at Harvard University and, in 2001, moved to the University of Wisconsin, Madison as an assistant professor of Chemistry. After spending seventeen years in Madison, he moved back to Boston in 2018. His current research interest includes quantum chemistry and statistical mechanics and their application to various chemical, biological and materials problems. Wenjun Xie is an Assistant Professor of Medicinal Chemistry at the University of Florida. He received his B.S. degree in chemistry and statistics in 2012 and his Ph.D. in physical chemistry in 2017 from Peking University, where he conducted research under the supervision of Professor Yiqin Gao. He subsequently completed postdoctoral training with Professor Bin Zhang at the Massachusetts Institute of Technology and Professor Arieh Warshel at the University of Southern California. His current research focuses on the development of artificial intelligence and computational chemistry approaches to understand enzyme catalysis and evolution.

• 1. Inferring conformational equilibria from sparse experimental data2. TBD3. Gaussian Process Regression and DeepMD models for simulating solution-phase and enzyme reactions4. Modern Computational Enzymology Methods for Nucleic Acid Catalysis5. Capturing Transition States of Enzyme Dynamics6. Deep learning approaches for identifying the reaction coordinates and mechanisms of enzyme catalysis7. Methods of walking in path space as applied to chemical reactions in enzymes8. TBD9. Using large language models for enzyme kinetics data extraction10. Multidimensional Mechanistic Profiling at Scale with High-Throughput Enzymology11. TBD12. Using CLEAN for new enzyme discovery13. Using EZSpecificity to expand the substrate border.14. GeoEvoBuilder-Driven Enzyme Engineering with Enhanced Activity and Thermostability