Journal of Physical Chemistry B, Vol.106, No.44, 11647-11657, 2002
Full optimization of linear parameters of a united residue protein potential
We apply the general protocol of parameter optimization (Lee, J.; Ripoll, D. R.; Czaplewski, C.; Pillardy, J.; Wedemeyer, W. J.; Scheraga, H. A. J. Phys. Chem. B 2001, 105, 7291) to the UNRES potential. In contrast to earlier works where only the relative weights of various interaction terms were optimized, we optimize all linear parameters of the potential. The method exploits the high efficiency of the conformal space annealing method in finding distinct low-energy conformations. For a given training set of proteins, the parameters are modified to make the nativelike conformations energetically more favorable than the non-native ones. Linear approximation is used to estimate the energy change due to the parameter modification. The parameter change is followed by local energy reminimization and new conformational searches to find the energies of nativelike and non-native local minima of the energy function with new parameters. These steps are repeated until the potential predicts a nativelike conformation as one of the low-energy conformations for each protein in the training set. We consider a training set of crambin (PDB ID 1ejg), 1fsd, and the 10-55 residue fragment of staphylococcal protein A (PDB ID 1 bdd). As the first check for the feasibility of our protocol, we optimize the parameters separately for these proteins and find an optimal set of parameters for each of them. Next, we apply the method simultaneously to these three proteins. By refining all linear parameters, we obtain an optimal set of parameters from which the nativelike conformations of the all three proteins are retrieved as the global minima, without introducing additional multibody energy terms.