Getting Started

Build Documentation

Rosetta Basics

Application Documentation

Scripting Interfaces

Development Documentation

Internal Documentation

How to Write Documentation

FAQ

Glossary

Options list

Back to Mover page.

SimpleGlycosylateMover

Table of Contents

MetaData

Mover created by Dr. Jared Adolf-Bryfogle (jadolfbr@gmail.com) and Dr. Jason Labonte (JWLabonte@jhu.edu)

PIs: Dr. William Schief (schief@scripps.edu) and Dr. Jeffrey Gray (jgray@jhu.edu)

Reference

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

Description

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.

Details

Autogenerated Tag Syntax Documentation:

Authors: Jared Adolf-Bryfogle (jadolfbr@gmail.com) and Jason W. Labonte (JWLabonte@jhu.edu) Mover to add specified glycosylations to a pose in the specified positions

References and author information for the SimpleGlycosylateMover mover:

SimpleGlycosylateMover Mover's author(s): Jared Adolf-Bryfogle, The Scripps Research Institute, La Jolla, CA [jadolfbr@gmail.com]

<SimpleGlycosylateMover name="(&string;)" glycosylation="(&string;)"
        glycosylations="(&string;)"
        position="(&refpose_enabled_residue_number;)"
        positions="(&refpose_enabled_residue_number_cslist;)"
        atom_name="(&string;)" weights="(&delimited_real_list;)"
        strip_existing="(&bool;)" ref_pose_name="(&string;)"
        idealize_glycosylation="(&bool;)" residue_selector="(&string;)" />
  • glycosylation: String specifying the glycosylation to add to this pose (IUPAC Glycan String) (or a file name containing the glycosylation with a .iupac name)
  • glycosylations: String or file name specifying multiple possible glycosylations to add to this pose (IUPAC Glycan String) (or a file name containing the glycosylation with a .iupac name) (will be sampled randomly
  • position: Position to add glycosylation
  • positions: Positions to add glycosylations
  • atom_name: Atom to which glycan is chemically linked
  • weights: Sampling weights corresponding to the provided set of glycans
  • strip_existing: Strip existing glycosylations from the pose
  • ref_pose_name: Name of saved reference pose
  • idealize_glycosylation: Idealize glycosylations on the pose?
  • residue_selector: . The name of a previously declared residue selector or a logical expression of AND, NOT (!), OR, parentheses, and the names of previously declared residue selectors. Any capitalization of AND, NOT, and OR is accepted. An exclamation mark can be used instead of NOT. Boolean operators have their traditional priorities: NOT then AND then OR. For example, if selectors s1, s2, and s3 have been declared, you could write: 's1 or s2 and not s3' which would select a particular residue if that residue were selected by s1 or if it were selected by s2 but not by s3.

See Also

RosettaCarbohydrate Apps and Components