Hello All- I have a peptide with an o-linked disaccharide that I would like to model and/or dock to a protein binding partner. I can generate the glycopeptide. So, I wanted to first try and manually dock it to the protein. For the manual docking, I was wondering if there is a tool for coot or another graphics program to apply a series of preferred conformation to the glycans (in relation to the protein side chain to which it is linked), somewhat like you would do for a side chain rotamer. This is pure ab initio modeling, ie. not into electron density. Anyone have a suggestion? Thanks in advance! -Todd
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