作者
Adam Liwo, Mey Khalili, Cezary Czaplewski, Sebastian Kalinowski, Stanisław Ołdziej, Katarzyna Wachucik, Harold A Scheraga
发表日期
2007/1/11
期刊
The Journal of Physical Chemistry B
卷号
111
期号
1
页码范围
260-285
出版商
American Chemical Society
简介
We report the modification and parametrization of the united-residue (UNRES) force field for energy-based protein structure prediction and protein folding simulations. We tested the approach on three training proteins separately:  1E0L (β), 1GAB (α), and 1E0G (α + β). Heretofore, the UNRES force field had been designed and parametrized to locate native-like structures of proteins as global minima of their effective potential energy surfaces, which largely neglected the conformational entropy because decoys composed of only lowest-energy conformations were used to optimize the force field. Recently, we developed a mesoscopic dynamics procedure for UNRES and applied it with success to simulate protein folding pathways. However, the force field turned out to be largely biased toward α-helical structures in canonical simulations because the conformational entropy had been neglected in the parametrization …
引用总数
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