New use case - comparison of docking poses about espsim HOT 3 CLOSED

Hi @Tonylac77, sorry for the late response, and thank you very much for your question!

In general, it is definitely possible to get shape and ESP similarities while conserving the docking poses, technically. In that case, you would only want to call GetEspSim() and GetShapeSim() where the molecular conformation should be the exact docking pose. Both functions only compute the similarity of the given pose, without any alignment. If you want to keep the geometry, but are ok with rotation and translation of the whole molecule to align, I can give some advice on that too. I can also give some advice on reading in the poses, depending on the format they are saved in.

So, technically it is rather easy and straightforward to get the scores. However, I cannot guarantee how useful the scores are, as I have not tested this use case at all (although we do plan to run some benchmarks in the future). I would be very interested to find out, though, so if you want to give it a try, I would be very grateful if you could report your observations.

If you do not get satisfactory results directly, you might also want to consider using better partial charges than the default ones, e.g. AM1-BCC (which is a separate software that we unfortunately cannot integrate directly, but it is straightforward to run on all poses and read them in with the esp-sim package), I can provide some guidance on that.

from espsim.

Hi, just wanted to add that we included some docking benchmarks and scripts in the new version of the manuscript, just in case you would like to take a look! Also, we now enable machine-learned partial charges, which perform pretty well in our docking benchmarks! Let me know if you have questions!

from espsim.

Hi @Tonylac77, I am closing this issue since I believe it was solved. Feel free to reopen or open a new issue if you have further questions!

from espsim.