Would anyone know how to create a glycosaminoglycan (heparan sulfate, chondroitin sulfate, hyaluronic acid) using pyrosetta?
You should be able to import the function core.pose.pose_from_saccharide_sequence and use, for example:
pose = pose_from_saccharide_sequence( "b-D-GlcpNS6S-(1->4)-b-L-GulpA-(1->4)-b-D-GlcpNS6S-(1->4)-b-L-GulpA" )
If you have any issues, e-mail me directly at JWLabonte@jhu.edu.
I should also note that Rosetta is not very good at handling the electrostatics of sulfates, though.
Perfect many thanks.