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Protocols

GlyProt specifications

Information


Unique identifier OMICS_18509
Name GlyProt
Interface Web user interface
Restrictions to use None
Input data A PDB ID.
Input format PDB
Computer skills Basic
Stability Stable
Maintained Yes

Maintainer


  • person_outline Andreas Bohne-Lang

Publications for GlyProt

GlyProt citations

 (17)
library_books

Escape of Hepatitis C Virus from Epitope I Neutralization Increases Sensitivity of Other Neutralization Epitopes

2018
J Virol
PMCID: 5899191
PMID: 29467319
DOI: 10.1128/JVI.02066-17

[…] son-Boltzmann solver (). The binding surfaces were calculated by using the Proteins, Interfaces, Structures, and Assemblies server (). Glycans were modeled by using the in silico glycosylation server GlyProt (). […]

library_books

Glycosylation of Hemagglutinin and Neuraminidase of Influenza A Virus as Signature for Ecological Spillover and Adaptation among Influenza Reservoirs

2018
Viruses
PMCID: 5923477
PMID: 29642453
DOI: 10.3390/v10040183

[…] de: 3LZG) and NA (PDB code: 4B7Q) together were used as the model for human influenza H1N1. After homology modeling, glycans were added onto the potential N-glycosylation sites in HA and NA using the Glyprot Server [,]. All N-linked glycans (N-glycans) were selected as the basic conformation and the structures were visualized by the PyMOL Molecular Graphics System, version 1.8, Schrödinger, LLC (N […]

library_books

Zo peroxidase: Crystal structure and sequence of a highly glycosylated peroxidase resistant to high concentrations of H2O2 from Japanese radish

2017
PMCID: 5857146
PMID: 29556562
DOI: 10.1016/j.bbrep.2017.09.008

[…] l to the 2FO − FC electron-density map. Program COOT was used for manual model building and addition of calcium ions, glycans and water molecules. Glycosylation sites were previously monitored using GlyProt . All further refinement was performed with PHENIX to a final Rwork/Rfree of 16.2/19.7%. Data collection and refinement statistics are summarized in . […]

call_split

Structures of Ebola Virus GP and sGP in Complex with Therapeutic Antibodies

2016
Nat Microbiol
PMCID: 5003320
PMID: 27562261
DOI: 10.1038/nmicrobiol.2016.128
call_split See protocol

[…] robity score, and the agreement of the model to the EM density as measured by the EMRinger score,.Energy minimized GlcNAc2Man3 glycans were added to the final c2G4/c13C6/GPΔTM protein structure using GlyProt. The glycan torsion angles were manually adjusted to fit into density and residues without supporting density were removed. The glycans were further refined into the density using Coot with to […]

library_books

Complementary LC MS/MS Based N Glycan, N Glycopeptide, and Intact N Glycoprotein Profiling Reveals Unconventional Asn71 Glycosylation of Human Neutrophil Cathepsin G

2015
Biomolecules
PMCID: 4598777
PMID: 26274980
DOI: 10.3390/biom5031832

[…] performed using PyMOL Molecular Graphic System, v1.3 (Schrödinger, LLC) and RasMol v2.7.5, respectively. N-glycans were modeled on Asn71 of nCG in silico using the default torsion angles provided by Glyprot []. The solvent accessibilities of Asn71 and the individual methionine residues of nCG were determined using NACCESS, a solvent accessibility determination program []. The atomic accessible ar […]

library_books

The Mechanism by which 146 N Glycan Affects the Active Site of Neuraminidase

2015
PLoS One
PMCID: 4534095
PMID: 26267136
DOI: 10.1371/journal.pone.0135487

[…] 2HTY-With-Glycan were created using the corresponding atomic coordinates of the fractional 146-N-glycan in 3NSS as a template, using a complex glycan structure type command that was obtained from the Glyprot Server (http://www.glycosciences.de/modeling/glyprot/) [].The structure of the NA tetramer was created from monomer structures by applying a VMD 1.9 matrix transformation using Tcl script []. […]


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GlyProt institution(s)
German Cancer Research Center Heidelberg, Central Spectroscopy–Molecular Modeling, Heidelberg, Germany
GlyProt funding source(s)
Supported by a grant from the German Research Council (Deutsche Forschungsgemeinschaft, DFG) within the digital library program.

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