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I want to perform a molecular docking between a protein of interest and several ligands. This membrane protein has a transmembrane domain composed of an alpha helix structure, which exerts it's function in a dimeric conformation, that is, by binding two identical proteins in its transmembrane domain. The crystal structure for this protein it's not available so it is necessary to design it ab initio. For this, we have the following working protocol:

  • Design of the monomeric 3D structure from the amino acid chain. FMAP software.

  • Obtaining the percentage of protein embedded in the membrane and its degrees of tilt. OMP.

  • Design of the dimeric structure. RosettaMP

  • Exploratory simulations for the selection and refinement of the dimeric model. CHARMM-GUI

The main problem I'm finding with this approach is that Rosetta software needs supercomputing capacity. I would like to know if there's a reliable server option for developting the dimeric structure.

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    $\begingroup$ +1 and welcome to our new community! Thank you for contributing your question here, and we hope to see much more of you!!! If you need access to supercomputing capacity, how about this or this or this? Is your question answered by those? $\endgroup$
    – Nike Dattani
    May 6, 2021 at 2:43
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    $\begingroup$ Thanks @NikeDattani. I´ll surely stick around here some more, looks promising $\endgroup$
    – SharkCaller
    May 21, 2021 at 18:08
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    $\begingroup$ As it has been almost 2 months now, are you able to say why those server options suggested in my last comment, are not helpful? $\endgroup$
    – Nike Dattani
    Jun 30, 2021 at 18:45

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