Phi/psi-chology: Ramachandran revisited.

By Gerard J. Kleywegt, T. Jones. 1996

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Citations in the corpus

Features and development of Coot (2010, neutral): “Kleywegt & Jones (1996) included the Ramachandran plot in the restraints during reﬁnement using X-PLOR (Bru¨nger, 1992) and reported that the number of Ramachandran outliers was reduced by about a third using moderate force constants.”
Conformation Dependence of Backbone Geometry in Proteins (2009, methodology): “As seen in Figure 2, these residues were distributed in F,J as has been seen for many wellfiltered data sets (Karplus, 1996; Kleywegt and Jones, 1996, Lovell et al., 2003).”
Implementing an X-ray validation pipeline for the Protein Data Bank (2012, methodology): “For more general reviews of the types of errors that can occur in protein crystal structures as well as of validation methods that can be used to detect (some of) these, we refer to the literature (Brändén & Jones, 1990; Kleywegt & Jones, 1995, 1996, 1997, 2002; Kleywegt, 2000, 2007, 2009).”
Use of knowledge-based restraints in phenix.refine to improve macromolecular refinement at low resolution (2012, unknown): “Ramachandran-plot restraints have been used previously by Kleywegt & Jones (1996) in X-PLOR (Brünger, 1992a), as well as in CNS (Brünger et al., 1998), both of which targeted the general-case Ramachandran plot.”
MolProbity’s Ultimate Rotamer-Library Distributions for Model Validation (2016, background): “18,27,37 An important question is how the new system will change rotamer analysis, specifically the number and identity of outliers.”
Self‐consistent method for density estimation (2009, methodology): “, 2003), and reconstruction of Ramachandran angle distributions (Kleywegt and Jones, 1996).”
A fresh look at the Ramachandran plot and the occurrence of standard structures in proteins (2010, methodology): “As was initiated for turn types (3), we will use a prime symbol (9) to represent a mirror image conformation.”
A New Generation of Crystallographic Validation Tools for the Protein Data Bank (2011, unknown): “Combinations of torsion angles, such as the main-chain f , c (Ramachandran) or side-chain c s (rotamers), are rarely restrained, so they remain extremely valuable for validation tests (Kleywegt and Jones, 1996).”