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Docking antibody to membrane protein

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Docking antibody to membrane protein

Hello, what are the general guidelines for docking, when one of the protieins is a transmembrane and its partner is supposed to dock to the extracellular part (e.g. antibody or ligand)? 

  • I suppose that the transmembrane one should be relaxed using MPFastRelax, whereas the extracellular using the standard REF15?
  • Which scoring function should be specified for docking?
  • Should one include any constraint to hide the intracellular and membrane part from docking or it's not necesary?
  • Are there any example protocols doing that?


Thank you in advance!

Post Situation: 
Thu, 2023-10-12 07:37

I am interested in this topic too. An example xml file for docking a soluble protein to a transmembrane one will be helpful. Everything i have tried so far creates all sorts of errors.

 The errors im getting from running the attached files are ,

ERROR: The SpanningTopology object in MembraneInfo is empty! and 

ERROR: Cannot split pose by membrane jump! Quitting... 

Thank you for helping out 

File attachments: 
Tue, 2023-10-17 09:58

I found a related thread Apparently docking a soluble protein to a TM one was not possible in 2020. Is it still the current status, or has there been any progress in the meantime?

Wed, 2023-10-18 07:57