Efficient generation of low-energy folded states of a model protein

A number of short simulated annealing runs are performed on a highly-frustrated 46-"residue" off-lattice model protein. We perform, in an iterative fashion, a principal component analysis of the 946 nonbonded interbead distances, followed by two varieties of cluster analyses: hierarchical and k-means clustering. We identify several distinct sets of conformations with reasonably consistent cluster membership. Nonbonded distance constraints are derived for each cluster and are employed within a distance geometry approach to generate many new conformations, previously unidentified by the simulated annealing experiments. Subsequent analyses suggest that these new conformations are members of the parent clusters from which they were generated. Furthermore, several novel, previously unobserved structures with low energy were uncovered, augmenting the ensemble of simulated annealing results, and providing a complete distribution of low-energy states. The computational cost of this approach to generating low-energy conformations is small when compared to the expense of further Monte Carlo simulated annealing runs. (C) 2003 American Institute of Physics.