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The UNRES Coarse-grained Model of Polypeptide Chains: Theory and Applications

 9, 2015
 
Title:The UNRES coarse-grained model of polypeptide chains: theory and applications
Reporter: Prof. Adam Liwo(Adam Liwo)
Time: Sep 17, 2015(Thursday)10:00 a.m.
Location: Room 610, CenTral Building
 
ABSTRACT
Coarse-grained force fields are of increasing importance in the simulations of biological macromolecules. In this talk, the physics-based UNited RESidue (UNRES) model and force field for the simulations of proteins will be described. The UNRES force field stems from the potential of mean force of polypeptide chains in water, in which the degrees of freedom not present in the model are averaged out. To determine the effective energy terms, the potential of mean force is expanded into the generalized Kubo cluster-cumulant series, which has enabled us to derive analytical expressions for the multibody terms, which couple backbone-conformational states to backbone hydrogen-bonding interactions, and are essential to reproduce regular secondary structures. The model is designed to run coarse-grained Langevin-dynamics simulations of proteins or find the most stable structures through global optimization of the effective energy surface. The model has been used successfully in protein-structure prediction, studying free-energy landscapes of proteins, simulation of folding pathways and kinetics, and simulating processes of biological interest. It has also been used in determining the mechanism of protein folding in the framework of the kink/soliton theory.
 
Curriculum Vitae
Dr. Jozef Adam Liwo has been a professor (tenure) and a head of laboratory of molecular modeling of chemistry department at the University of Gdansk (Poland). Dr. Liwo obtained his Ph.D in physical and theoretical chemistry from the University of Gdansk in 1989. During 1992-1994, he was a postdoctoral fellow of Prof. Harold Scheraga at the Cornell University in the United States. Dr. Liwo has taken some honors and awards including the “Master” subsidy for distinguished professors from the Foundation for Polish Science (2013), a specialist member of the Biophysics and Biochemistry Committee of the Polish Academy of Sciences (2012), 1st Degree Awards for outstanding research from the Polish Ministry of National Education (1989, 1995, 2001). Dr. Liwo has published more than 200 original papers and 10 review articles in ISI journals with more than 3000 citations (as of January 2015). Dr. Liwo has an h-index 36.
 
Contact:School Office of Physics (68913163)
Inviter: Prof. Jianfeng He
Website:http://physics.bit.edu.cn/
Release date:2015-10-27