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

enter image description here

Thanks in advance.

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    $\begingroup$ +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. $\endgroup$ – Nike Dattani Apr 16 at 1:22
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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 $2.0 \overset{\circ}{\mathrm{A}}$

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  • $\begingroup$ Thank you so much, and if I haven't a cocrystallized ligand, What can I do? $\endgroup$ – Giu Apr 16 at 19:19
  • $\begingroup$ 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? $\endgroup$ – Giu Apr 16 at 19:21
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    $\begingroup$ 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). $\endgroup$ – Camps Apr 16 at 19:26
  • $\begingroup$ Can you explain me wich method can I use to validate the docking? and if it's possible using maestro. many thanks $\endgroup$ – Giu Apr 16 at 20:34
  • $\begingroup$ You should post your doubt in a separate question. I will be happy to help. $\endgroup$ – Camps Apr 18 at 14:19

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