3 years ago

Maximum Likelihood Calibration of the UNRES Force Field for Simulation of Protein Structure and Dynamics

Maximum Likelihood Calibration of the UNRES Force Field for Simulation of Protein Structure and Dynamics
Stanisław Ołdziej, Wioletta Żmudzińska, Adam Liwo, Anna Hałabis, Paweł Krupa, Harold A. Scheraga
By using the maximum likelihood method for force-field calibration recently developed in our laboratory, which is aimed at achieving the agreement between the simulated conformational ensembles of selected training proteins and the corresponding ensembles determined experimentally at various temperatures, the physics-based coarse-grained UNRES force field for simulations of protein structure and dynamics was optimized with seven small training proteins exhibiting a variety of secondary and tertiary structures. Four runs of optimization, in which the number of optimized force-field parameters was gradually increased, were carried out, and the resulting force fields were subsequently tested with a set of 22 α-, 12 β-, and 12 α + β-proteins not used in optimization. The variant in which energy-term weights, local, and correlation potentials, side-chain radii, and anisotropies were optimized turned out to be the most transferable and outperformed all previous versions of UNRES on the test set.

Publisher URL: http://dx.doi.org/10.1021/acs.jcim.7b00254

DOI: 10.1021/acs.jcim.7b00254

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