Optimization of the UNRES force field by hierarchical design of the potential-energy landscape. 3. Use of many proteins in optimization

The application of hierarchical optimization of protein potential-energy landscapes to optimize the UNRES force field using multiple training proteins is reported. The resulting force field trained on a set of four proteins gives good medium-resolution predictions of the structures of most of the alpha- and the alpha + beta-proteins, but still could not handle nontrivial beta-motifs sufficiently well.