EVALUATION OF 2 PROCEDURES FOR SELECTING STARTING CONFORMATIONS FOR ENERGY MINIMIZATION OF PEPTIDES

In an effort to develop a computationally efficient method of finding low-energy minima of blocked dipeptides, we have evaluated two methods for generating starting conformations. The ''representative'' method involves (1) plotting points representing the locations of single-residue energy minima on two-dimensional conformation maps with the dihedral pairs phi-psi, chi-chi2, chi3-chi4, etc., as coordinates, (2) choosing a representative dihedral angle pair from each of the clusters of points on these maps, and (3) combining these representative single-residue points to form dipeptide starting conformations. The ''concatenation method'' uses all combinations of single-residue minima. Applying these two methods to blocked His-Arg and to blocked Asp-His, we found that (1) both methods successfully located what we assume to be the global minimum, (2) the two methods yielded essentially the same statistical averages of conformational properties, and (3) many low-energy minima located by each method were not located by the other method, although the representative method located many more low-energy minima than did the concatenation method.