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.