I have to validate one of my docking protocol but I haven't a co-crystalized ligand. There is a way to validate it? Thanks in advance.
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1$\begingroup$ I edited the question to make it more general. Also, you can not validate a docking result with the same docking program without a co0cristalized ligand. $\endgroup$– Camps ♦Commented Apr 19, 2021 at 9:36
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$\begingroup$ Ah ok, and how can I do? $\endgroup$– GiuCommented Apr 19, 2021 at 9:39
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2 Answers
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Using different score functions
One way to validate the docking results is scoring your poses using a different score function. You will need to use one of this two methods:
- Use another docking software: in this case you have to do a score-in-place procedure, i.e. not re-docking your ligands, just score the poses. For example, if you work with GLIDE (that is the software that do the docking in the Schrodinger suite, not MAESTRO), you can use AUTODOCK-VINA, PLANTS, GOLD, etc.
- Use scoring software: these software have the only purpose to score the poses using score functions obtained from experimental data. Examples are XSCORE, AGL-SCORE, DLSCORE, etc.
If you obtain the same pose rank using a different score functions, then your docking results are good (without any bias due to the software used)
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$\begingroup$ Thank you so much. I have onother question: Can I use this two methods also for validate the docking protocol with a co-crystallized ligand? $\endgroup$– GiuCommented Apr 19, 2021 at 10:21
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$\begingroup$ Sure. But the idea to use a co-crystallized ligand is to use it with the same software you did your docking (without the need of third party software). $\endgroup$– Camps ♦Commented Apr 19, 2021 at 10:34
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$\begingroup$ How can I perform a score-in-place procedure with autodock? It is a new software for me and I don't Know how procede. Thanks in advance for help $\endgroup$– GiuCommented Apr 20, 2021 at 11:21
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Different docking programs can be tried for a benchmark.
The re-docking technique can be used: you separate the receptor experimental structure from the ligand and re-dock back the ligand into the receptor with different docking programs.
Docking can be evaluated with an RMSD calculation. However, no measurement is robust by itself, so the optimum might also be to visualize the key interactions that the ligand makes with the receptor and compare them with the literature.
Classical positional distance-based measurement is the RMSD calculation while the interaction-based measurement is the investigation of key residues in the specific case of study. For instance, a specific class of receptors have key residues that interact with endogenous ligands.
We have recently developed a free web server for positional distance-based and interaction-based analysis of docking results (https://pegasus.lbic.unibo.it/pacdock/index.php).
I hope you find it useful.
