I'm modelling a GPCR based on rhodopsin as a template. The sequence
similarity is relatively low (<20%), but the conserved residues are
located in the 7 Transmembrane
Helices, and the alignment of the TMs is obvious. It is assumed that
the topology is well conserved (more so than expected from the sequence
similarity), because of the known folding pattern in the GPCR-family.
The question is this:
Is there any way to assign greater weight to the conserved residues
in the TM-regions in the distance constraints in the pdf, or in any other
way assure that the information about the conserved residues won't get
lost in the optimization?
Dan Thomas Major (at Dr. B. Fischer's lab)