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

Question

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

Thanks in advance.

Answer 1

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.
3. Use the ligand pose from the downloaded complex as your reference structure.
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).
• Select the reference structure from the crystal structure you downloaded.
• 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 $2.0 \overset{\circ}{\mathrm{A}}$