个人简介

Ph.D.(2001) State University of New York at Stony Brook

研究领域

Bioanalytical/Cellular Biochemistry and Drug Discover/Chemical Biology/Computational Chemistry and Biochemistry/Structural Biology

Although experimental biochemical & biophysical measurements have been developed rapidly, understanding and designing complex biomolecular systems is still quite challenging. Computer simulation based on captured biopolymer structures (by X-ray, NMR etc.) can be an essential complementary technique to catalyze our exploration of microscopic world. Due to the complexity of biological systems in both length scale and time scale, biomolecular simulation need to be both functional and efficient; facing this challenge, my research interest targets the development and application of state-of-art multi-spectrum atomistic simulation techniques including QM/MM calculation, free energy simulation, conformation path simulation, motion analysis etc., to understand the hidden nature of complex biological phenomena. Specifically, my research program includes three directions: 1. First principle based protein and ligand design; 2. Simulation study of multi-timescale biochemical & biophysical events such as DNA repair, motion- coupled biomolecular recognition, and enzymatic reactions; (Figure below shows one of systems studied previously) 3. Development of simulation techniques to describe complex systems and enhance efficiency of biomolecular simulations.

近期论文

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Zheng, L. and Yang, W.* Practically efficient and robust free energy calculations: Double integration orthogonal space tempering. J. Chem. Theor. Comput. 2011, in press Riera, T. V., Zheng, L. Q., Josephine, H. R., Min, D., Yang, W.*, and Hedstrom, L.* Allosteric activation via kinetic control: Potassium accelerates a conformational change in IMP Dehydrogenase. Biochemistry 2011, 50:85088518 Min, D. H., Chen, M. E., Zheng, L. Q., Jin, Y. H., Schwartz, M. A., Sang, Q. X. A., and Yang, W.* QM/MM molecular dynamics sampling in explicit environments via an orthogonal space random walk based strategy. J. Phys. Chem. B 2011, 115, 3924-3935 Lee, S., Chen, M., Yang, W.*, and Richards, N. G. J.* Sampling Long Timescale Protein Motions: OSRW Simulation of Active Site Loop Conformational Free Energies in Formyl-CoA:Oxalate CoA Transferase. J. Am. Chem. Soc. 2010, 132, 7252-7253 Zheng, L., Chen, M., and Yang, W.* Random walk in orthogonal space to achieve efficient free energy simulation of complex systems. Proc. Natl. Acad. Sci. USA 2008, 51, 20227-20232