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Glycan Reader specifications


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


  • person_outline Wonpil Im

Publication for Glycan Reader

Glycan Reader citations


Effects of N Glycan Composition on Structure and Dynamics of IgG1 Fc and Their Implications for Antibody Engineering

Sci Rep
PMCID: 5627252
PMID: 28978918
DOI: 10.1038/s41598-017-12830-5

[…] -GlcNAc, 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 ( The TIP3P model was used for explicit water molecules. The cubic system size was determined to have at least 15 Å from the protein in eac […]


Very Low Density Lipoprotein of Metabolic Syndrome Modulates Gap Junctions and Slows Cardiac Conduction

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

[…] osylated 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. […]


Solution NMR characterization of chemokine CXCL8/IL 8 monomer and dimer binding to glycosaminoglycans: structural plasticity mediates differential binding interactions

PMCID: 4692082
PMID: 26371375
DOI: 10.1042/BJ20150059

[…] ld. The GAG segments from the HADDOCK models were read into SYBYL-X 2.1.1 (Tripos), the sulfate groups removed and the glucosamine residues converted into glucose. This structure was submitted to the Glycan Reader [] of the CHARMM-GUI server ( to assign atom types, patched using the modified topology file via the psfgen plugin in VMD 1.9.2 [] to generate the psf and pdb f […]


The solution structures of native and patient monomeric human IgA1 reveal asymmetric extended structures: implications for function and IgAN disease

PMCID: 4692083
PMID: 26268558
DOI: 10.1042/BJ20150612

[…] glycosidic bond.This ‘assembled’ PTerm455 structure was prepared for energy minimization through the addition of H atoms and the optimization of steric overlaps within the crystal structure using the glycan reader component of CHARMM-GUI [,] and the CHARMM36 force field [–]. Disulfide bridges were included between Cys23–Cys93 and Cys139–Cys199 in each light chain and Cys22–Cys98, Cys145-Cys204, Cy […]


Enhanced Conformational Sampling Using Replica Exchange with Concurrent Solute Scaling and Hamiltonian Biasing Realized in One Dimension

J Chem Theory Comput
PMCID: 4463548
PMID: 26082676
DOI: 10.1021/acs.jctc.5b00243

[…] ycopeptides 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 […]


Developing the IVIG biomimetic, Hexa Fc, for drug and vaccine applications

Sci Rep
PMCID: 5224519
PMID: 25912958
DOI: 10.1038/srep09526

[…] o 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 in the tex […]

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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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