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I did a docking job and got a score of -5.69 kcal/mol and a value for MM-GBSA of -60 kcal/mol.

I should analyze these results for my thesis but do not know how to comment on them. Does anyone have any insight about what this number might mean?

Also on interactions, I wonder what can be said? Are there plots of the data that would be appropriate to include?

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You can analyze your docking results in two ways.

First way is looking for the score function your program uses. For some score functions, lower value indicates better interactions and for others, higher values indicate better interactions. Also,, look for the decomposition of the score. Normally, the score is composed by different type of interaction/penalties like Coulomb electrostatic interaction, van der Waals interaction, H-bond interaction, etc. This partition scheme will help you to understand which is the main mechanism of interaction between your ligand and the protein. This should be the main way to get conclusions about how the interaction occurs.

The second way is by visually inspecting the 2D Interaction diagram. To produce those diagrams, you need to use another software like Maestro, LigPlot+, LeView, PoseView, and Protein-Ligand Interaction Profiler just to cite a few. Not all the relevant information about the interactions is shown in this 2D diagrams.

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    $\begingroup$ Many thanks. At moment I just use maestro suite $\endgroup$ – Anastasia01 May 18 at 18:51
  • $\begingroup$ In this case can I tell that, even though, the docking score is not very good the mm-gbsa shown that my ligand could be taken into conideration as a possible Inhibitor of my target? – Anastasia01 12 mins ago Delete $\endgroup$ – Anastasia01 May 18 at 19:12
  • $\begingroup$ If you did the docking using Maestro, you had used one of two methods, GLIDE or IFD (that uses GLIDE). GLIDE is a well tested docking software that its results are reliable even when the protein is kept fixed. On the other hand, IFD gave some flexibility to the protein. So, having positive values of g-score (GLIDE Score) is a bad sign. $\endgroup$ – Camps May 18 at 20:37
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    $\begingroup$ Sorry, I made a mistake. The glide score is -5,600. $\endgroup$ – Anastasia01 May 18 at 20:49
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    $\begingroup$ Many thanks for your help :) $\endgroup$ – Anastasia01 May 18 at 21:40
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Docking results can be analyzed in a number of ways by looking at various geometric parameters, such as a distances, angles and dihedrals. These are then typically compared against "ideal" values, such as a those at the transition state. Graphs typically contain a parameter on each axis with the results and ideal points plotted. Interactions can mean various things, such as H-bonds and pi-interactions. Comment made before revisions to initial question

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    $\begingroup$ Thank you so much, but i don't undestand if my score is good or not in relation to the result of mm-gbsa $\endgroup$ – Anastasia01 May 18 at 18:29
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    $\begingroup$ I am so sorry but I am a beginner and i have much thing to learn $\endgroup$ – Anastasia01 May 18 at 18:30
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    $\begingroup$ @Anastasia01 No problem, we all have to start somewhere! One thing to keep in mind with docking, the best pose is not always the reactive pose. As far as precision goes for these calculations, they are typically system dependent in their ability to be accurate. A lot of care has to go into setting the system up to get accurate results. $\endgroup$ – kskinnerx16 May 18 at 18:38
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    $\begingroup$ @Anastasia01 Results also get trickier to interpret when a non-native ligand is studied. Comparisons to the native ligand will be required, or a reference ligand if the native is not known. $\endgroup$ – kskinnerx16 May 18 at 18:41
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    $\begingroup$ You cannot compare the score with the MM-GBSA. Also, you can not compare the score obtained with different software. $\endgroup$ – Camps May 18 at 18:42
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A good way to proceed is to use a control in your experiment as with modelling experiment in general. You can, for example, use the co-crystalized ligand or a well-know inhibitor (something experimentally established with IC50 value for example) of your protein of interest. The values obtained with that ligand in your docking/MMGBSA calculations will serve as guide for comparison...

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