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pdb-care specifications

Information


Unique identifier OMICS_21253
Name pdb-care
Alternative name PDB CArbohydrate REsidue check
Restrictions to use None
Input format PDB
Computer skills Basic
Version 2.0
Stability Beta
Maintained Yes

Maintainers


  • person_outline Thomas Lutteke
  • person_outline Claus-W von der Lieth

Publications for PDB CArbohydrate REsidue check

pdb-care citations

 (13)
library_books

Structure of a cleavage independent HIV Env recapitulates the glycoprotein architecture of the native cleaved trimer

2018
Nat Commun
PMCID: 5955915
PMID: 29769533
DOI: 10.1038/s41467-018-04272-y

[…] ermined by MR with PGV19 (determined in this study) and BG505 SOSIP.664+PGT122 from PDB 4TVP. The structures were refined using Phenix and model building performed in Coot. MolProbity, Privateer, and pdb-care were used for structure validation. The refinement statistics are reported in Supplementary Table . […]

library_books

Structural analysis of glycoproteins: building N linked glycans with Coot

2018
Acta Crystallogr D Struct Biol
PMCID: 5892875
PMID: 29652253
DOI: 10.1107/S2059798318005119

[…] Privateer was used for the validation of all carbohydrate models. Unfortunately, the output files created by Coot could not be parsed by pdb-care from glycosciences.de (Lütteke & von der Lieth, 2004) so this could not be used for additional validation. […]

library_books

Bacterially derived synthetic mimetics of mammalian oligomannose prime antibody responses that neutralize HIV infectivity

2017
Nat Commun
PMCID: 5693931
PMID: 29150603
DOI: 10.1038/s41467-017-01640-y

[…] y chains of PGT128 (PDB 3TV3) as the starting model. Strong Fo-Fc density for the glycoside was apparent in the resulting map. Phenix was used for refinement and model building was conducted in Coot. Pdb-care, was used to validate carbohydrate geometry, and the structure was validated with MolProbity. The final structure had no Ramachandran outliers and 97.5% of residues fell within the favored r […]

library_books

Two faced Fcab prevents polymerization with VEGF and reveals thermodynamics and the 2.15 Å crystal structure of the complex

2017
MAbs
PMCID: 5627596
PMID: 28816592
DOI: 10.1080/19420862.2017.1364825

[…] All models were validated with MolProbity and PDB_REDO., Carbohydrates were validated with pdb-care and Privateer. Figures were prepared with PyMOL Molecular Graphics System (Version 1.3, Schrödinger, LLC). Atomic coordinates have been deposited in the Protein Data Bank under accession code […]

library_books

Strategies for carbohydrate model building, refinement and validation

2017
Acta Crystallogr D Struct Biol
PMCID: 5297920
PMID: 28177313
DOI: 10.1107/S2059798316016910

[…] when modelling carbohydrate structures at low resolution. This correspondence was met with a letter from the PDB in which they acknowledged the issue and highlighted the availability of tools such as PDB-CARE (Lütteke & von der Lieth, 2004) for nomenclature validation. More recently, another study reported a worrying situation affecting ring conformation (Agirre, Davies et al., 2015), using N-glyc […]

library_books

High Resolution Crystal Structures Elucidate the Molecular Basis of Cholera Blood Group Dependence

2016
PLoS Pathog
PMCID: 4833353
PMID: 27082955
DOI: 10.1371/journal.ppat.1005567

[…] h MarvinSketch (ChemAxon.com), using isomeric SMILES strings for the individual monosaccharides. The final ligand PDB and library files were created using PRODRG [], and were checked for errors using pdb-care (glycosciences.de/tools/pdbcare []). The oligosaccharides were only modeled into the binding sites if clear electron density of at least three residues was present. Occupancies were refined b […]

Citations

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pdb-care institution(s)
German Cancer Research Center, Central Spectroscopic Department, Heidelberg, Germany
pdb-care funding source(s)
Supported by a grant from the German Research Council (Deutsche Forschungsgemeinschaft: DFG) within the digital library program.

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