Use of non-crystallographic symmetry in protein structure refinement.

By Gerard J. Kleywegt. 1996

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Citations in the corpus

Towards automated crystallographic structure refinement with phenix.refine (2012, methodology): “If insufficient care is taken in defining the NCS groups, the above method may be counterproductive (Kleywegt & Jones, 1995; Kleywegt, 1996, 1999, 2001; Usón et al., 1999).”
Features and development of Coot (2010, neutral): “9) is a variation of the Ramachandran plot that is used to highlight NCS Screenshot of a Kleywegt plot (Kleywegt, 1996) showing Ramachandran differences between two NCS-related chains by connecting lines (angles in degrees).”
FragBag, an accurate representation of protein structure, retrieves structural neighbors from the entire PDB quickly and accurately (2010, methodology): “The gold-standard answer includes neighbors found by a best-of-six structural aligner (using SSAP (26), STRUCTAL, DALI (27), LSQMAN (28), CE, and SSM); this expensive computation was done previously (10).”
ElNémo: a normal mode web server for protein movement analysis and the generation of templates for molecular replacement (2004, methodology): “Root mean square distances (RMSD) between the normal mode perturbed models and a second (not necessarily sequence-identical) structure are computed by a rigid body superposition using the lsqman software (25).”
Structure of a bacterial multidrug ABC transporter (2006, methodology): “Alignments and the open state model ClustalW (Thompson et al, 1994) was used for Figure 1C. LSQMAN (Kleywegt, 1996) was used for all structural alignments.”
Flexible torsion-angle noncrystallographic symmetry restraints for improved macromolecular structure refinement (2014, methodology): “Alternatively, constraint-based approaches improve the data-toparameter ratio by requiring NCS-related regions to be identical, such as the methods described in Hendrickson (1985) and Kleywegt (1996).”
Current developments in Coot for macromolecular model building of Electron Cryo‐microscopy and Crystallographic Data (2019, methodology): “To compare NCS-related chains in the context of the Ramachandran plot, the Kleywegt plot can be used (Figure 3b), where NCS-related residues from two chains are plotted on the Ramachandran plot connected by an arrow.(42) By default, the 50 most distant residues are plotted.”
Checking your imagination: applications of the free R value. (1996, background): “At high resolution one may be able to refine NCS-related molecules independently [12, 19 ].”