RNA backbone is rotameric

By L. Murray, W. Bryan, Arendall Iii, David C Richardson, Jane S. Richardson. 2003

223 citations recorded by the source corpus.

Subfields: Materials Chemistry, Molecular Biology

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In Molecular Biology

Citations in the corpus

Assessment of three-dimensional RNA structure prediction in CASP15 (2023, positive): “28 The assessment also considered the coordinate comparison metric TM-score as computed in RNA-Align 29 and the Mean of Circular Quanti-ties 30 to assess accuracy in the torsion angle space.”
RNA Structure Refinement using the ERRASER-Phenix pipeline (2013, unknown): “Previous research (22, 23) shows that most of the RNA backbone ‘suites’ (sets of two consecutive sugar puckers with 5 connecting backbone torsions falls into 54 rotameric classed.”
Model validation: local diagnosis, correction and when to quit (2018, background): “Dividing RNA backbone into sugar-to-sugar units (suites) works better than using chemical nucleotides and shows that the RNA backbone is ‘rotameric’ (Murray et al., 2003), while that of DNA is not.”
MolProbity: More and better reference data for improved all‐atom structure validation (2018, background): “56 These backbone conformers, with a few updates, (see Methods) are a validation criterion in MolProbity.”
Computational Methods for RNA Structure Validation and Improvement. (2015, background): “shown to be rotameric (Murray et al., 2003), a study that was extended by theRNAOntology Consortium to describe 54 distinct conformations commonly adopted by the RNA backbone (Richardson et al.”
MolProbity: all-atom structure validation for macromolecular crystallography (2009, unknown): “…problems than do proteins, with the bases and phosphates located well and the rest of the sugar-phosphate backbone very prone to errors (Word, Lovell, Richardson et al., 1999; Murray et al., 2003), since it has many torsion variables and rather indistinct electron density at moderate resolutions.”
FR3D: finding local and composite recurrent structural motifs in RNA 3D structures (2007, background): “Several different representations of RNA backbone conformations have been introduced to search for, analyze, and classify recurrent RNA 3D conformations [9,10,18,37,38,41,43].”
Pairing a high-resolution statistical potential with a nucleobase-centric sampling algorithm for improving RNA model refinement (2021, background): “…in this work is tailored speci ﬁ cally to RNA interactions that were dominant by orientation-dependent base-pairing and stacking interactions 30 with rotameric backbone 31 , in contrast to dominant distance-dependent hydrophobic interactions 32 with rotameric sidechains 33 in protein folding.”
KING (Kinemage, Next Generation): A versatile interactive molecular and scientific visualization program (2009, methodology): “Another is clustering the conformations of RNA, where (coincidentally) seven dihedral angles define the backbone conformation between two bases.(17) For the RNA analysis, we originally used different sets of three angles to make many different 3-D plots.”
MOLPROBITY: structure validation and all-atom contact analysis for nucleic acids and their complexes (2004, background): “All-atom contacts (including all hydrogens) provide new information that is independent of the target functions used in refinement and that can sensitively and easily locate such problems (4,7).”
RNA backbone: consensus all-angle conformers and modular string nomenclature (an RNA Ontology Consortium contribution). (2008, methodology): “Murray et al. (2003) proposed the sugar-to-sugar ‘‘suite’’ unit (see Fig.”
RNA-Puzzles: a CASP-like evaluation of RNA three-dimensional structure prediction. (2012, background): “MolProbity performs several automatic analyses, from checking the lengths of H-bonds present in the model to validating the compliance with the rotameric nature of the RNA backbone (Murray et al. 2003).”