Glycan Reader specifications

Information


Unique identifier OMICS_18917
Name Glycan Reader
Interface Web user interface
Restrictions to use None
Input data A structure files with glycans.
Input format PDB
Computer skills Basic
Stability Stable
Maintained Yes

Maintainer


  • person_outline Wonpil Im <>

Publication for Glycan Reader

Glycan Reader in publications

 (5)
PMCID: 5627252
PMID: 28978918
DOI: 10.1038/s41598-017-12830-5

[…] fc-n297q, and fc/man8/n297q were generated by removing glycan residues or mutating n297 to q297., to generate simulation input files for each system, we used quick md simulator integrated with glycan reader at the charmm-gui website (www.charmm-gui.org). the tip3p model was used for explicit water molecules. the cubic system size was determined to have at least 15 å from the protein […]

PMCID: 5608762
PMID: 28935953
DOI: 10.1038/s41598-017-11416-5

[…] variant, an initial energy minimization of the glycoprotein was performed using a steepest descent algorithm. finally, the electrostatic potential surface of the glycoprotein was built using glycan reader., the data was expressed as means ± sd unless indicated otherwise and n indicates the number of cell samples or mice. one-way anova and tukey’s multiple comparisons test were used […]

PMCID: 4463548
PMID: 26082676
DOI: 10.1021/acs.jctc.5b00243

[…] and contribute to the epitopes of selected hiv-neutralizing antibodies., the initial sct model was built from the combination of two crystal structures (pdb id 4dqo() and 4fqc()), and the glycan reader module in charmm-gui, was used to generate the m5 model on the basis of the crystal structure 4nco. each molecule was solvated in a cubic tip3p water box with a dimension of 56 å × 56 å […]

PMCID: 5224519
PMID: 25912958
DOI: 10.1038/srep09526

[…] both heavy chains of the fc domain. finally, the hinge and two residue mutations that enable oligomerization into the hexa-fc were generated. the initial files for the simulation were obtained with glycan reader. the simulations ran for ~150 ns, and the trajectory analyzed after the protein had equilibrated after the first 30 ns. to distinguish between the two configurations described […]

PMCID: 3597548
PMID: 23516343
DOI: 10.1371/journal.pcbi.1002946

[…] (3d) structures in the pdb has not been studied., in this work, using the pdb crystal structures that contain n-glycans, we examined the conformational variability in various n-glycans. using glycan reader , an automatic sugar recognition algorithm that we developed, all n-linked glycoprotein structures were obtained from the pdb and sorted by their n-glycan sequence. pdb entries […]


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Glycan Reader institution(s)
Department of Biological Sciences and Bioengineering Program, Lehigh University, Bethlehem, PA, USA; Leadership Computing Facility, Argonne National Laboratory, Argonne, IL, USA
Glycan Reader funding source(s)
Supported by NSF DBI-1707207, NIH GM087519, NIH GM103695, and XSEDE MCB070009.

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