Solvation and randomization in ALLOSMOD glycan modeling
I am trying to use allosmod package in MODELLER for ab initio modeling of glycans as described in the paper "All-atom ensemble modeling to analyze small-angle x-ray scattering of glycosylated proteins" (Structures 2013. DOI: 10.1016/j.str.2013.02.004).
I have two questions regarding the glycan modeling method, about which I could not find any prior discussions in this forum. My questions are:
(1) In the glycan modeling methods section of the paper, it is mentioned that "initial structures were generated by addition of glycan chains with ideal geometries derived from CHARMM, followed by a 1angstrom randomization of the full atomic coordinates". I am assuming this randomization is the same as the randomize_xyz function of MODELLER. However, since templates are not being provided by the user for the glycans, how are the sugar ring puckerings and dihedral angles correctly reproduced even after such large random deviations?
(2) My understanding is, in MODELLER, the solvation information is taken implicitly from the template provided. However, since the glycans are modeled template-free, is there any explicit treatment of solvation, or is the optimization done in vacuum?
Thanks, -Srirupa
On 5/20/19 12:07 PM, Chakraborty, Srirupa via modeller_usage wrote: > I am trying to use allosmod package in MODELLER for ab initio modeling > of glycans
allosmod isn't part of Modeller, but it does use Modeller as one of its dependencies. See the AllosMod docs at https://allosmod.readthedocs.io/en/latest/ for more details. You can also dig through all the source code at GitHub to see exactly what is going on: https://github.com/salilab/allosmod-lib/
> (1) In the glycan modeling methods section of the paper, it is mentioned > that "initial structures were generated by addition of glycan chains > with ideal geometries derived from CHARMM, followed by a 1angstrom > randomization of the full atomic coordinates". I am assuming this > randomization is the same as the randomize_xyz function of MODELLER. > However, since templates are not being provided by the user for the > glycans, how are the sugar ring puckerings and dihedral angles correctly > reproduced even after such large random deviations?
AllosMod adds suitable restraints for each sugar residue using the CHARMM forcefield, as per https://salilab.org/modeller/FAQ.html#8. See top_all_glyco.lib and par_all_glyco.lib at https://github.com/salilab/allosmod-lib/tree/master/data.
> (2) My understanding is, in MODELLER, the solvation information is taken > implicitly from the template provided. However, since the glycans are > modeled template-free, is there any explicit treatment of solvation
No.
Ben Webb, Modeller Caretaker
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Chakraborty, Srirupa -
Modeller Caretaker