Figure 2

The lowest-lRMSD conformation achieved through MEA and the AMW energy function is shown for three selected target sequences. The chosen sequences capture the range of lowest lRMSDs achieved, varying from 3 to 5Å. The lowest-lRMSD conformation is drawn in red and is superimposed over the corresponding native structure of each sequence, which is drawn in blue. Rendering is performed with the Visual Molecular Dynamics (VMD) software [70], using the NewCartoon rendering representation which highlights secondary structures. The camera is positioned so as to highlight structural differences between the lowest-lRMSD conformation and the corresponding native structure.