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Protocols

ValLigURL specifications

Information


Unique identifier OMICS_06368
Name ValLigURL
Interface Web user interface
Restrictions to use None
Input format PDB
Computer skills Basic
Stability Stable
Maintained Yes

Maintainer


  • person_outline Kleywegt GJ

Publication for ValLigURL

ValLigURL citations

 (3)
call_split

Mix and diffuse serial synchrotron crystallography

2017
PMCID: 5668862
PMID: 29123679
DOI: 10.1107/S2052252517013124
call_split See protocol

[…] n Coot, followed by further rounds of refinement in phenix.refine to convergence. Polygon (Urzhumtseva et al., 2009) and MolProbity (Chen et al., 2010) were used for validation of the final model and ValLigURL (Kleywegt & Harris, 2007) was used to check the geometry of the refined CTO molecule.To assess the influence of the starting lysozyme model, structure refinement was also carried out in both […]

library_books

Structural Insights into the Polyphyletic Origins of Glycyl tRNA Synthetases*♦

2016
PMCID: 4938167
PMID: 27226617
DOI: 10.1074/jbc.M116.730382

[…] try of the GSAd ligand was adjusted to that observed in PDB code 3hy0 (structure of catalytic fragment of E.coli AlaRS in the complex with GlySA). Validation of the GSAd ligand was performed with the ValLigURL server (). Figures were prepared with PyMOL (The PyMOL Molecular Graphics System, Version 1.7.4, Schrödinger, LLC). […]

library_books

A New Generation of Crystallographic Validation Tools for the Protein Data Bank

2011
PMCID: 3195755
PMID: 22000512
DOI: 10.1016/j.str.2011.08.006

[…] ecular mechanics calculations, as in the PRODRG server (). Yet another alternative is to compare the geometry of a ligand with any other instances of that same ligand in the PDB, an approach taken in ValLigURL (). wwPDB deposition sites currently use the ideal geometry, stereo-chemistry, and standard names defined in the chemical components dictionary () when ligands are deposited that already occ […]

Citations

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ValLigURL institution(s)
Department of Cell and Molecular Biology, Uppsala University, Biomedical Centre, Uppsala, Sweden

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