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- person_outline Kleywegt GJ
Publication for ValLigURL
Mix and diffuse serial synchrotron crystallography
[…] 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 […]
Structural Insights into the Polyphyletic Origins of Glycyl tRNA Synthetases*♦
[…] 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). […]
A New Generation of Crystallographic Validation Tools for the Protein Data Bank
[…] 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 […]
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