AboutDownloadsForumsWikiSource CodeIssuesNews

Release Name: Starting Structure 5

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.