help on job https://mobyle.rpbs.univ-paris-diderot.fr/data/jobs/MTiAutoDock/B21524431250095.

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Hi,
I have several problems trying to work with your - otherwise VERY NICE - MTiAutoDock pipeline.
My job ID: https://mobyle.rpbs.univ-paris-diderot.fr/data/jobs/MTiAutoDock/B21524431250095

First of all, I know it is a complicated protein target to dock to as it is a homology-modeled HOMOtrimer (SWISS-MODEL-derived).
So, I expect ligands to bind to cavities in ALL monomers with the same / similar binding modes. But that is not the case. MTiAutoDock first of all exclusively docks to TWO of the 4 subunits. Why?

Next: The downloaded data archive does not contain anything I can make use of - except the .csv table.
All html files won’t load - or better said: will load telling me that cookies need to be enabled to view the webpage. Well, I tried latest browser versions of both Firefox and Microsoft Edge. Same result. And: Cookies were enabled. :wink:

What I need is files able to be loaded into ChimeraX or PyMOL directly visualizing the protein plus the docked ligands plus a binding energy information table (that I can derive from the job webpage but not from the webpages downloaded in the results archive (except for .csv probably - but this file is too uncomfortable to handle to be really practically useful)). Not just my input files (receptor protein plus ligand).

I found a floppy disk symbol. Clicking on that opens another html page where I can MANUALLY download files. When I open the receptor protein in ChimeraX and then additionally load the .pdbqt file of e.g. the first row it appears that the ligand is posed properly in what appears to represent a binding pocket on the complex’s surface. That’s nice, but VERY tedious to individually download all .pdbqt files. And later I can barely associate th binding energies (nice would be objects in ChimeraX / PyMOL with energy as object names).
It was only one ligand which I tested. Do all binding modes from the first row .pdbqt file (lowest energy) correspond to the same ligand binding with the same energy at different positions/modes to the protein?
It would probably be useful to export these positions directly as .pdbqt file (or PDB or whatever) named with the binding-energy?

I appreciate your work.
Best regards & I hope you may find time to answer my questions,
Michael.

Session information:

  • id: 0fbe1e986e6fd76208c877d24684df27
  • email: weberm@posteo.de
  • activated?: True
  • authenticated?: True

Job information: