Sample Run

In the following, you can see an example NMSim run for Adenylate Kinase from PDB 4AKE. Please see the results below. The original web results can be seen here.

>> Download PDB file (4AKE) for which the NMSim calculations were performed <<

Example:

Results:

4AKE_trajectory.pdb.gz
A PDB file containing the conformations of the trajectory.

Examples for Jmol:

Color-coded representation of the Rigid Cluster Decomposition. The largest rigid cluster is shown in blue.



20 conformations extracted at equally spaced intervalls from the NMSim trajectory. The starting structure is depicted in blue, the ending structure in green, all other conformations corresponding to the secondary structure elements. Simulated movements of the protein can be animated within the JMol Plugin using Mouse -> Right click -> Animation -> Play.


Graph showing the Cα atom RMSD to the starting structure over the trajectory.


Graph showing the Cα atom root mean-square fluctuations over the trajectory.