Job Title:
1omp
Cutoff distances for building ENM from PDB1:
Rc(aa-aa)=10.0
Rc(aa-dntp)=12.5
Rc(dntp-dntp)=15.0
PDB1 (first PDB file) is used to build ENM and compute normal modes.
PDB2 (second PDB file) is used for validation.
Map sequence from PDB1 to PDB2 (370/370 residues are mapped).
Table 1. The following DCs are fitted using 10 lowest normal modes from PDB1:
| DC # | residue pair | initial distance | target distance | weight |
| 1 | Y16,I234 | 18.93 | 11.70 | 1.00 |
| 2 | K45,F338 | 19.89 | 12.67 | 1.00 |
Table 2. Contribution of each of the 10 lowest normal modes to the DC-fitted (overlap1) and observed (overlap2) structural displacements:
| mode # | overlap1 | overlap2 |
| 1 | -0.64 | -0.65 |
| 2 | 0.73 | 0.68 |
| 3 | -0.06 | -0.10 |
| 4 | 0.09 | 0.06 |
| 5 | 0.05 | 0.06 |
| 6 | -0.00 | -0.05 |
| 7 | -0.08 | -0.07 |
| 8 | -0.03 | -0.04 |
| 9 | 0.02 | 0.06 |
| 10 | 0.02 | 0.06 |
The result of the 100-step iterative fitting process is shown in this figure:
red curve - amplitude of structural displacement from the initial structure (PDB1) in RMSD;
green curve - maximal deviation from the target distances;
blue curve - RMSD from the known end-state structure (PDB2)
The final structural model of the unknown state: download PDB file
The trajectory of fitting DCs: download PDB file (view movie)
Note: the amino acid residues tagged in the DCs are assigned a temperature factor of 100 so they can be easily identified.