Ph.D., University of Duisburg, Germany
We have been focusing on the development and application of molecular mechanics-based computational methods to investigate the interactions among biomolecules, with an emphasis on the significance of biomolecular dynamics, so as to provide a more solid basis for unraveling molecular interactions. Molecular dynamics simulations facilitated with high performance computing are performed to provide the dynamical information not available by X-ray crystallography and nuclear magnetic resonance experiments, and such information will further assist computational drug design of novel chemical entities. Besides, our lab also develops methods to predict the previously unknown targets of natural products or even marketed drugs. One of such examples is that in 2007 we successfully predicted that statins are also inhibitors of HDAC, which plays an important role in the epigenetic mechanism of carcinogenesis, which lead to the design and synthesis of new generation statins that have significantly improved anticancer efficacy. In addition to topics directly related to computational drug design, recently we also employed molecular dynamics simulations to investigate the molecular mechanism of molecular motors, including ATP synthases and FtsZ, conformational transitions in the telomeric DNA quadruplexes, and the alternative access mechanism of membrane transporters at the sub-molecular level.
A Curvilinear-Path Umbrella Sampling Approach to Characterizing the Interactions Between Rapamycin and Three FKBP12 VariantsFrontiers in Molecular Biosciences, Jul 08, 2022
Recovery of the poisoned topoisomerase II for DNA religation: coordinated motion of the cleavage core revealed with the microsecond atomistic simulation.Nucleic Acids Res., Jul 06, 2015