# How to compare structural results by superposition and compute RMSD to validate docking?

I wonder how to use this panel to validate docking? I tried and the results are a disaster:

• +1 But please can you take a screenshot of the screen rather than a photograph with your camera? Please press "print screen" and paste the image into here. It will look way better than this does. – Nike Dattani Apr 16 at 1:22

Here are the steps to validate your docking protocol (not your docking results):
(Note: this is one way to do the validation, not the only one)

1. Download a crystal structure of a complex (ligand/substrate + protein) from Protein Data Bank server.
Note: It is recommended to use the same protein (not necessarily the same structure) you used in your docking.
2. Do a re-docking using the ligand/protein you downloaded under the same conditions you did your docking.
4. Align the reference structure with all the poses you obtain in the re-docking (or at least, the best scored poses).
5. Calculate the RMSD between the reference structure and the selected poses.

From the Panel you show:

• You can add all the re-docking poses to the Workspace or just select them in the project table. If added to the workspace, chose the Workspace option (if selecting the project table, the other option).
To conclude that the docking protocol is reliable, the desired max(RMSD) should be below $$2.0 \overset{\circ}{\mathrm{A}}$$