Protein Folding by Molecular Dynamics with the United-Residue Force Field

	Special Guest Lectures
	Protein Folding by Molecular Dynamics with the United-Residue Force Field
	Harold Scheraga
	Cornell University, Todd Professor of Chemistry, Emeritus
	Life Sciences Annex A101 March 15, 2006 - 03:45 pm
Abstract: Molecular Dynamics (MD) calculations of protein folding pathways with an all-atom force field cannot cover the time scale (milliseconds to seconds) of this process. In order to achieve stable folding trajectories by MD, the time step for solving Newton's equations is of the order of femtoseconds; therefore, it would require an impossible amount of computer time to reach the millisecond time scale. The all-atom approach can reach only the nanosecond time scale with currently available computer power. This problem is being overcome by using a united-residue (UNRES) instead of an all-atom force field. In UNRES, the fast degrees of freedom are averaged out, enabling one to follow the folding process further in time than with the all-atom approach. The UNRES methodology, and its application to Langevin dynamics will be discussed.

Speaker's Bio: Harold Scheraga received his Ph.D. from Duke University, and was an American Chemical Society Postdoctoral Fellow at Harvard Medical School, after which he joined Cornell University as a faculty member. Currently, he is a member of many professional organizations including the National Academy of Sciences, American Academy of Arts and Sciences, and the New York Academy of Sciences. He received a Doctor Honoris Causa from Technion, the Israel Institute of Technology, the National University of San Luis (Argentina), and the University of Gdansk (Poland). He has received several awards by the American Chemical Society (the Nichols Medal, the Hirschmann Award in Peptide Chemistry, the Repligen Award for Chemistry of Biological Processes, and the Eli Lilly Award in Biochemistry, to name a few. He has published more than one thousand scientific articles, and is an active editorial & advisory board member of numerous scientific journals.

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