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forlilab / Ringtail

Package for storage and analysis of virtual screenings run with AutoDock-GPU and AutoDock Vina
GNU Lesser General Public License v2.1
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Two question for documentation #61

Open xavgit opened 1 day ago

xavgit commented 1 day ago

Hi, in the documentation ( https://ringtail.readthedocs.io/en/stable/index.html ) in the command line interface section there is the following statement: "Be cautious when adding results from multiple screening runs, since some target information is checked and some is not." It is possible to receive some examples about what I should be cautious? For the scatterplot in the section Create scatterplot highlighting ligands passing filters it is possible to describe what it is its meaning? For example the reasons why there are red, blue and green circles? Sorry, I don't have any experience with this type of plot.

Many thanks.

Saverio

diogomart commented 19 hours ago

Hi, Just replying to your first question here, and maybe @maylinnp or @althea-hansel can elaborate or correct what I'm writing. Ringtail tail was designed to have one receptor, not more, per database. The interactions with the receptor are filtered using chain ID and residue numbers, thus conflicts would be nearly unavoidable if results originate from multiple receptors. But it is impossible to guarantee that docking results originate from a single receptor because the docking output files (".dlg" from autodock-gpu or ".pdbqt" from vina) do not have enough information for that.

xavgit commented 2 hours ago

Hi, thanks for the reply. Sorry for the request of the meaning of the red circles as I had missed the line in the documentation where there was the explanation. If possible, another question. Can be planned for Vina the output of the docking results in .dlg format? In this format there are the cluster histogram and rmsd table sections that provide interesting informations and , also, the processing with ringtail can be made in more uniform way.

Thanks.

Saverio

diogomart commented 1 hour ago

That would have been nice from the start, but now many people expect PDBQT out of vina, if we changed that it would be backwards incompatible. Also Vina doesn't store clustering data internally.