Release Name: Starting Structure 8
In order to determine whether the starting configuration is native-like each structural characteristic of the starting structure is compared to the native state. A configuration is native-like if it compares to the native state within one standard deviation of each metric in the native state simulations. Second, we analyzed folding by monitoring the collective relaxation of a set of structural elements to native-like configurations. We computed the RMSD of each helical carbon in the snapshot from an energy-minimized native state structure. We also computed the distances between the three phenylalanine residues, F6, F10, and F17, which comprise the hydrophobic core in the folded structure. A structure was considered to be folded by the structural metric if it met the following criteria: (1) C RMSD of helix 1 less than 1.56 Å. (2) C RMSD of helix 2 less than 0.33 Å. (3) C RMSD of helix 3 less than 0.85 Å. (4) F6–F10 ring centroid distance less than 7.17 Å. (5) F6–F17 ring centroid distance less than 6.76 Å. (6) F10–F17 ring centroid distance less than 6.55 Å.