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I want to perform a molecular docking between several ligands and the transmembrane domain of a protein.

For this protein I only have the amino acid sequence, so it's necessary to do two things:

  • Determine which part of the aminoacid sequence belongs to the transmembrane domain (see this)

  • Model the 3D structure based on this aminoacid sequence (trRosetta software)

I would like to know if this little protocol that I have established (with the two softwares) is rigorous and the conclusions of a study based on it could be taken into account.

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