Biowulf High Performance Computing at the NIH
Glycosylator: framework for the rapid modeling glycans and glycoproteins.

Glycosylator is a Python framework for the identification, modeling and modification of glycans in protein structure that can be used directly in a Python script through its API or GUI. The GUI allows for a quick visual inspection of the glycosylation state of all the sequons on a protein structure. Modeled glycans can be further refined by a genetic algorithm for removing clashes and sampling alternative conformations. Glycosylator can also identify specific three-dimensional (3D) glycans on a protein structure using a library of predefined templates.


Important Notes

Interactive job
Interactive jobs should be used for debugging, graphics, or applications that cannot be run as batch jobs.

Allocate an interactive session and run the program. Sample session:

ssh -Y
[user@biowulf]$ sinteractive --mem=4g
[user@@cn3109 ~]$ module load glycosylator
Run the Glycosylator GUI:
[user@@cn3109 ~]$

Use the Glycosylator API:
[user@@cn3109 ~]$ python
>>> import os
>>> import glycosylator as gl
>>> myGlycosylator = gl.Glycosylator(os.path.join(gl.GLYCOSYLATOR_PATH, 'support/toppar_charmm/carbohydrates.rtf'), os.path.join(gl.GLYCOSYLATOR_PATH, 'support/toppar_charmm/carbohydrates.prm'))>>> myGlycosylator.builder.Topology.read_topology(os.path.join(gl.GLYCOSYLATOR_PATH, 'support/topology/'))
>>> myGlycosylator.builder.Topology.read_topology(os.path.join(gl.GLYCOSYLATOR_PATH, 'support/topology/'))
>>> myGlycosylator.load_glycoprotein(os.path.join(gl.GLYCOSYLATOR_PATH, 'support/examples/env_4tvp.pdb'))
@> 5309 atoms and 1 coordinate set(s) were parsed in 0.04s.
>>> myGlycosylator.build_glycan_topology(patch = 'NGLB')
Exit the current session:
[user@cn3144 ~]$ exit
salloc.exe: Relinquishing job allocation 46116226
[user@biowulf ~]$