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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)
Bar-Ilan University 
Ramat-Gan, Israel