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
This mover is created to do denovo modeling and refinement of glycans. It does this through iteratively sampling and building out the glycan trees from their roots. By default (without a passed residue selector), it selects ALL glycan residues in the pose. Please see the GlycanResidueSelector for selecting particular glycan trees and the GlycanLayerSelector for particular glycan layers.
Note that the defaults used internally by the modeler are now the optimal defaults found in the upcoming paper. The plethora of options here are mostly for benchmarking. The only two options you should need are
scorefxn (and optionally
-refine for re-modeling glycans)
Autogenerated Tag Syntax Documentation:
Author: Jared Adolf-Bryfogle (firstname.lastname@example.org) Brief: A protocol for optimizing glycan trees using the GlycanSampler by computationally growing glycans from the roots out to the trees.
It is recommended to use this modeling algorithm in conjunction with the -beta scorefunction, as this was shown to work best for modeling glycans. QUECHING
By default, we model all glycans simultaneously. First, all glycan roots (the start of the tree), and slowly unvirtualize all glycan residues, while only modeling each layer. Alternatively, we can choose a particular glycan tree, run the algorithm, and then choose another glycan tree randomly until all glycan trees have been optimized. Here, we call this quenching.
Draw a tree on a paper. We start with the beginning N residues, and work our way out towards the leaves. Layers are defined by the glycan residue distance to the rooot. This enables branching residues to be considered the same layer conceptually and computationally, and allows them to be modeled together.
You do not need a ResidueSelector passed in. It will select all glycan residues automatically. However, if you do, you must only pass in glycan residues. See the GlycanResidueSelector and the GlycanLayerSelector for a very easy way to select specific glycan trees and residues.
References and author information for the GlycanTreeModeler mover:
GlycanTreeModeler Mover's author(s): Jared Adolf-Bryfogle, Institute for Protein Innovation (IPI), Boston, MA [email@example.com]
<GlycanTreeModeler name="(&string;)" refine="(false &bool;)" glycan_sampler_rounds="(100 &non_negative_integer;)" quench_mode="(false &bool;)" layer_size="(&non_negative_integer;)" window_size="(&non_negative_integer;)" rounds="(&non_negative_integer;)" use_conformer_probs="(false &bool;)" use_gaussian_sampling="(true &bool;)" force_virts_for_refinement="(false &bool;)" idealize="(false &bool;)" final_min_pack_min="(true &bool;)" min_rings="(false &bool;)" cartmin="(false &bool;)" hybrid_protocol="(true &bool;)" shear="(true &bool;)" match_window_one="(true &bool;)" root_populations_only="(false &bool;)" kt="(ℜ)" residue_selector="(&string;)" scorefxn="(&string;)" />