# 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. 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).
• Under RMSD option, select Compute without changing structures, to keep all the structures as they are (without changing their conformation). The other option will only add the RMSD to a column in the project table.
• Under the Choose method, select the one corresponding to the whole structures (all atoms).

To conclude that the docking protocol is reliable, the desired max(RMSD) should be below $$2.0 \overset{\circ}{\mathrm{A}}$$

• Thank you so much, and if I haven't a cocrystallized ligand, What can I do?
– Giu
Apr 16 at 19:19
• I run the re-docking and I perform superposition for my complex protein-ligand and RMSD values are over 4A. There is somethingto do for fix?
– Giu
Apr 16 at 19:21
• You can not use your own results to do the validation in this way. If you don't have a cocrystalized ligand for your protein, you can look for a protein of the same family. Or just, move to other validations method (using other score functions, other docking method).
– Camps
Apr 16 at 19:26
• Can you explain me wich method can I use to validate the docking? and if it's possible using maestro. many thanks
– Giu
Apr 16 at 20:34
• You should post your doubt in a separate question. I will be happy to help.
– Camps
Apr 18 at 14:19