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In a project, we performed some virtual screening calculations in order to predict inhibitors, and then purchased the compounds and tested them in the lab. One of them was a very good TK inhibitor (IC50 nM).

However, when we processed the results we realized that the presence of this particular compound in the original list of virtual screening hits was due to errors in the original calculations (it was added to the list by random factors, not by docking score).

So now we are writing the paper and we wonder how to argue this. We can not just tell the story like in this post (it was discovered by randomness or by our error). How would you argue this?

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    $\begingroup$ It was in your negative control set and it worked. I have had a lot of random mutations in my library designs which I did not plan on end up working. You just say it in the results section and don't try and matriculate on it too long. That is only possible if you have real molecules from the docking data that also worked. If that is so, you can definitely add this as a fluke and no one will argue. However, if it is the sole result and conclusion, it may be much harder to spin a high impact manuscript. $\endgroup$ – jwillis0720 Jun 22 '17 at 6:42
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    $\begingroup$ I'm voting to close this question as off-topic because it is about the process of submission of papers to journals and not about biology itself. Any answer is also subjective. $\endgroup$ – David Jun 22 '17 at 8:03
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    $\begingroup$ @David yes, Academia might be a better home for this. On the other hand, an understanding of the basic biological concepts involved is helpful for answering. I think it could go both ways. $\endgroup$ – terdon Jun 22 '17 at 9:58
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Be honest (and possibly split the papers).

If the compound was identified as an error and you want to include in a paper describing the process of your simulation and the effectiveness of the predicted inhibitors, you'd have to do so as a sort of negative control for your calculations (unless there is some way to reproduce/rationalise why it showed up randomly). Since this is the only good inhibitor you have, you'd have to conclude that your calculation isn't much better than chance, or explain why it is better even though you found a better inhibitor by chance. If you have reason to argument that your calculations are good and make sense then exclude the 'random' inhibitor from that paper. You can the write an individual paper about a good inhibitor, the fact that you found it by chance isn't that important anymore.

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