RNA backbone: consensus all-angle conformers and modular string nomenclature (an RNA Ontology Consortium contribution).

By Jane S. Richardson, B. Schneider, L. Murray, Gary J. Kapral, R. Immormino, J. Headd, David C Richardson, D. Ham, Eli Hershkovits, Loren Dean Williams and 5 more. 2008

252 citations recorded by the source corpus.

Subfields: Genetics, Materials Chemistry, Molecular Biology

How researchers see this paper

The researchers whose trusted networks rank it highest, strongest advocate first. Every researcher gets a different order.

In Genetics

1. Matthew L. Baker

In Materials Chemistry

1. Paul D. Adams
2. Pavel V. Afonine
3. Randy J. Read
4. T. C. Terwilliger
5. Nigel W. Moriarty
6. T. Croll
7. Nathaniel Echols
8. A. McCoy

In Molecular Biology

1. Paul D. Adams
2. Pavel V. Afonine
3. Randy J. Read
4. T. C. Terwilliger
5. Nigel W. Moriarty
6. Nathaniel Echols
7. A. McCoy
8. T. Croll

Citations in the corpus

• Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix (2019, background): “RNA ribose pucker outliers are diagnosed by a simple relationship between the well fit 30 phosphate and glycosidic bond direction (Richardson et al., 2008), which also enables puckerspecific geometry targets in refinement (Adams et al., 2010).”
• MolProbity: all-atom structure validation for macromolecular crystallography (2009, unknown): “The RNA Ontology Consortium has defined a two-character nomenclature and an initial set of 54 favorable RNA backbone conformers (Richardson et al., 2008).”
• The Phenix Software for Automated Determination of Macromolecular Structures (2011, background): “At low resolution (worse than 3Å), information from the core of a related structure is very valuable, and the regularity of helices and β sheets (and of base-pairs and ribose puckers for RNA[75]) always turns out to be greater than it appears.”
• FARFAR2: Improved de novo Rosetta prediction of complex global RNA folds (2020, unknown): “structures (Leontis and Zirbel, 2012), which is 15% larger and more diverse than the previous default fragment library from 2009 (Richardson et al., 2008).”
• A New Generation of Crystallographic Validation Tools for the Protein Data Bank (2011, unknown): “Therefore, some further definitions and tests of ribose pucker and of backbone torsion-angle conformations have been collaboratively developed by the RNA Ontology Consortium (Richardson et al., 2008).”
• Flexible torsion-angle noncrystallographic symmetry restraints for improved macromolecular structure refinement (2014, background): “…i.e. correlated ’/ conformations (Ramachandran & Sasisekharan, 1968), amino-acid side-chain rotamers (Lovell et al., 2000), and RNA backbone conformations (Richardson et al., 2008) etc., which allow a limited number of restraints to govern the coordinated movement of related structural elements.”
• 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.”
• Recent developments in phasing and structure refinement for macromolecular crystallography (2009, methodology): “Recently, validation criteria have been developed for carbohydrates [60] and for RNA backbone [61 ], as well as a promising new evaluation of under-packing in proteins [62 ].”