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Release Name: Starting Structure 2

Release Notes
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.
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