New parameters for the refinement of nucleic acid-containing structures.

By G. Parkinson, J. Vojtěchovský, L. Clowney, A. Brunger, Helen M. Berman. 1996

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Citations in the corpus

MOLPROBITY: structure validation and all-atom contact analysis for nucleic acids and their complexes (2004, background): “While existing torsion angle analyses (1,2) are substantially correct, errors in one or more angles, resulting in impossible conformations, are common (3,4).”
Structure of the CAP-DNA complex at 2.5 angstroms resolution: a complete picture of the protein-DNA interface. (1997, methodology): “The higher resolution, as well as the use of an updated DNA parameter file (Parkinson et al., 1996), provide an improved model for the complex and each of its components.”
MolProbity: all-atom structure validation for macromolecular crystallography (2009, unknown): “Protein backbone parameters were derived from Engh & Huber (2001) and nucleic acid backbone parameters from Parkinson et al. (1996).”
Structure quality and target parameters (2006, methodology): “Restraints derived from the CSD have come into widespread use for protein (Engh & Huber, 1991; Brünger, 1993; Priestle, 1994) and nucleic acid (Parkinson et al., 1996) refinement; since their derivation, the database has grown from some 80 000 structures to around 200 000.”
Xplor‐NIH for molecular structure determination from NMR and other data sources (2018, background): “The default force field includes bonds and angles designed to agree with the Engh and Huber parameter set56 for proteins and those of Parkinson et al.57 for nucleic acids, with improper dihedral angles used to uniquely define tetrahedral centers and to restrain rigid regions, such as aromatic rings.”
AceDRG: a stereochemical description generator for ligands (2017, background): “For amino acids and nucleic acids the ‘ideal’ values have been tabulated a number of times (Engh & Huber, 1991, 2001; Parkinson et al. , 1996).”
A New Generation of Crystallographic Validation Tools for the Protein Data Bank (2011, background): “Bond lengths and bond angles are slightly affected by sugar pucker, but 4 s outliers can be suitably evaluated from standard values (Parkinson et al., 1996), and occasional incorrect chirality of sugar substituents or strong deviation from base planarity can be ﬂagged, with proper attention to…”
RNA backbone: consensus all-angle conformers and modular string nomenclature (an RNA Ontology Consortium contribution). (2008, background): “The Web resources also include a set of atomic coordinates for each of the 46 defined suite conformers (plus the eight ‘‘wannabe’’ conformers described in the Materials and Methods), with close to ideal bond lengths and angles (Gelbin et al. 1996; Parkinson et al. 1996).”