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patrickbryant1 / Umol

Protein-ligand structure prediction
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Selection of the interaction sites and pLDTT score #15

Closed velocirraptor23 closed 5 months ago

velocirraptor23 commented 5 months ago

Hi Patrick,

I was wondering what in your experience would be a good selection on the interaction sites. I have noticed a selection has an impact on the outcome, for instance between 10 and 7 A. Another question would be if I test different sites from the same protein, the pLDTT could give a kind of score about the probably binding site?

Thanks a lot,

Cesar

patrickbryant1 commented 5 months ago

Hi Cesar,

I think your reasoning is correct. Note that we have added a pocket-free version of Umol that you can try also. The pocket version should be better though.

Hope this helps!

Patrick

velocirraptor23 commented 5 months ago

Hi, Thanks for your answer. What would be different with pocket-free, Does it sample the whole protein?

patrickbryant1 commented 5 months ago

Yes, see https://github.com/patrickbryant1/Umol/blob/master/predict.sh. I would still define the target site and use the pocket version though - just a tip.

velocirraptor23 commented 5 months ago

Thanks for your reply. I close this tread now.

Best wishes,

Cesar