报告人：Dr. Kenneth M. Merz, Jr. (Michigan State University)
报告时间：2018年12月4日下午4:00
报告地点：逸夫楼10楼报告厅
报告人简介：
Kenneth M. Merz, Jr. is an American biochemist and molecular biologist currently the Director, Institute for Cyber-Enabled Research and the Joseph Zichis Chair at University of Michigan-Ann Arbor and Editor-in-Chief of American Chemical Society’s Journal of Chemical Information and Modeling. As a highly cited expert in his field for the last 10 years, he shares a wide range of research interests in computational chemistry, biomolecular science and biology.
报告摘要：
Energy sampling against biomolecular ensembles has been of significant interest for several decades. Given the intricate nature of the internal energies of a biomolecular system, the multi-dimensional integral of the partition function is analytically inaccessible. This has lead to the development and application of numerical approximations for molecular ensemble sampling and partition function calculation. Unfortunately, these methods are often quite slow and computationally expensive. We have addressed the sampling problem by using a novel, patent-pending methodology termed “Movable Type” (MT) which is conceptually analogous to the way the movable type printing press works. By separating the inter/intra-molecular energy into pair potentials, the MT method simulates the molecular energies through pair potential sampling and (re)combination. In the MT algorithm, we have devised rules to progressively decompose a molecular system into components (as the printing forme) with independent integrals over pairwise distances between the components. In this study, the MT algorithm is validated against several benchmark sets demonstrating that it is competitive with other, much slower methods in the prediction of the free energy of ligand binding, small molecule conformational free energy surface search, and protein:ligand docking. Since the method works in seconds (vs. hours or days for conventional methods), the investigator can use the method to quickly study protein:ligand binding on the free energy surface.
- Bansal, N.; Zheng, Z.; Song, L. F.; Pei, J.; Merz Jr., K. M. The Role of the Active Site Flap in Streptavidin/Biotin Complex Formation. J. Am. Chem. Soc. 2018, 140, 5434–5446.
- Zhong, H. A.; Santos, E. M.; Vasileiou, C.; Zheng, Z.; Geiger, J. H.; Borhan, B.; Merz Jr., K. M. Free Energy Based Protein Design: Reengineering Cellular Retinoic Acid Binding Protein II Assisted by the Moveable-Type Approach. J. Am. Chem. Soc. 2018, 140, 3483–3486.
