Accuracy and reliability of the scaling-relaxation method for loop closure: an evaluation based on extensive and...

The accuracy and reliability of the recently proposed scaling-relaxation method for loop closure were examined by using extensive conformational sampling. For each of the eight heptapeptides chosen to represent a variety of protein conformations, 1,000-2,000 conformations were sampled. Each segment contained 14 rotatable backbone dihedral angles. The average root mean square deviations (RMSDs) between the predicted and the native conformations were 0.7 angstrom for the backbone and 1.2 angstroms for the side chain atoms. These predictions were substantially more accurate than the previous predictions (1.1 angstroms for the backbone and 2.2 angstroms for the side chain atoms) of the same eight protein segments based on limited conformational sampling (100 conformations for each segment). Large prediction errors mostly occurred at polar and surface side chains that are unlikely to have any meaningful conformation. Moreover, the reliability of seven of the eight predictions was demonstrated with their energy-RMSD and stability-RMSD correlations of the low-energy conformations, where the conformational stability was estimated by using the multiple copy simultaneous sampling method.