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Growing Glycans in Rosetta: Accurate de novo glycan modeling, density fitting, and rational sequon design Jared Adolf-Bryfogle, J. W Labonte, J. C Kraft, M. Shapavolov, S. Raemisch, T. Lutteke, F. Dimaio, C. D Bahl, J. Pallesen, N. P King, J. J Gray, D. W Kulp, W. R Schief bioRxiv 2021.09.27.462000; https://doi.org/10.1101/2021.09.27.462000
The SimpleGlycosylateMover allows one to glycosylate poses with the glycan of interest at specified positions. This is incredibly useful, as most glycans are unresolved in crystal structures. This is usually the starting point for modeling carbohydrates attached to proteins. It is extremely quick, and can be used right before the GlycanRelaxMover in order to both create and model the glycans in a single Rosetta run.
If a glycan is already present, we will delete the glycan before building the new glycan. Currently, we do not copy any torsions onto the new glycan. This is being worked on.
The mover can deal with a few different types of glycan names including full IUPAC names, files with the full IUPAC names, and short common names such as 'man9' or 'man5'.
Multiple names can be passed to the mover (with an optional set of weights), where for each position, we will sample on the possible glycosylations. This can be useful for heterogeneous positions, such as those found in the HIV envelope protein.
The Glycans should be modeled after glycosylation. One can idealize the torsions of the carbohydrate residues during glycosylation using conformer data we use for Glycan Relax. This option is 'idealize_glycosylations'. Even with this idealization, the structure will still need to be modeled properly. See GlycanRelaxMover for more information on modeling the resulting glycan.
See Working With Glycans for more.
Autogenerated Tag Syntax Documentation:
References and author information for the SimpleGlycosylateMover mover:
SimpleGlycosylateMover Mover's author(s): Jared Adolf-Bryfogle, The Scripps Research Institute, La Jolla, CA [firstname.lastname@example.org]
<SimpleGlycosylateMover name="(&string;)" glycosylation="(&string;)" glycosylations="(&string;)" position="(&refpose_enabled_residue_number;)" positions="(&refpose_enabled_residue_number_cslist;)" weights="(&delimited_real_list;)" strip_existing="(&bool;)" ref_pose_name="(&string;)" idealize_glycosylation="(&bool;)" residue_selector="(&string;)" />
Posethat uses sequons and cosubstrates for specific biological enzymes.