Geometric nomenclature and classification of RNA base pairs.

By Neocles Leontis, Eric Westhof. 2001

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Citations in the corpus

RNA-Puzzles: a CASP-like evaluation of RNA three-dimensional structure prediction. (2012, background): “The systematization of the knowledge about RNA architecture and interactions (Leontis and Westhof 2001) to gain a handle on the rapid increase in the number and size of RNA molecules with published structures available in public databases (Berman et al. 2000); 4.”
SimRNA: a coarse-grained method for RNA folding simulations and 3D structure prediction (2015, background): “…pseudobonds (level 1 of the base moiety representation) define the position and orientation of the base moieties and they approximate the Watson–Crick, Hoogsteen and sugar edges that can be used to represent all major interactions made by bases with each other as well as with the back-bone (31,32).”
FR3D: finding local and composite recurrent structural motifs in RNA 3D structures (2007, methodology): “Basepairs are classified according to the geometric categories introduced by Leontis and Westhof [32].”
RNA backbone: consensus all-angle conformers and modular string nomenclature (an RNA Ontology Consortium contribution). (2008, background): “1e and 0a prefer GA and 7a and 4b prefer _A, because A bases are uniquely good at the various noncanonical base-pair geometries (Leontis and Westhof 2001) needed in the second position of those four stack-switch conformations; those base pairs usually use Hoogsteen/WC edges in 1e or 7a, but Hoogstee”
New metrics for comparing and assessing discrepancies between RNA 3D structures and models. (2009, background): “4B), and relative atomic motion that is handled by discretizing the base–base interactions using symbolic annotation (Gendron et al. 2001; Leontis and Westhof 2001; Lemieux and Major 2002; Yang et al. 2003).”
Anticodon-like loop-mediated dimerization in the crystal structures of HDV-like CPEB3 ribozymes (2023, background): “Comparative sequence analysis suggests that P1 from the human CPEB3 ribozyme is closed by a wobble C•A pair (also found in sloth, armadillo, and dolphin), while other mammals, including the chimpanzee, present a cis Watson-Crick C-G bp (Webb and Luptak 2011).”
An enumerative stepwise ansatz enables atomic-accuracy RNA loop modeling (2011, methodology): “In each of these three cases, the high accuracy of the SWA model is reflected not only in low rmsd to the experimental loops but also complete recovery of the base pair and base stack geometries as classified in the Leontis – Westhof scheme (23) (see SI Appendix , Table S5).”
New prediction categories in CASP15 (2023, background): “25 Given two sets of interactions, one for the model and 27,28 It is worth noting that model-independent measures are known to overinflate scores for compressed models with unrealistic geometries.”
Use of knowledge-based restraints in phenix.refine to improve macromolecular refinement at low resolution (2012, positive): “To simplify the parameter syntax, the Saenger classification (Saenger, 1984) is used to annotate bonding patterns in RNA, while DNA uses the system of Leontis & Westhof (2001).”
The non-Watson-Crick base pairs and their associated isostericity matrices. (2002, background): “more edge-to-edge hydrogen bonds belong to one of 12 geometric families ( 7 ).”
3DNA: a versatile, integrated software system for the analysis, rebuilding and visualization of three-dimensional nucleic-acid structures (2008, background): “Whereas the complementary strands of double-helical DNA associate almost exclusively through canonical, Watson–Crick base pairing, RNA incorporates both Watson–Crick and noncanonical base pairs, including interactions of the bases with the 2′-hydroxyl group unique to the ribose suga”
RNA-Puzzles toolkit: a computational resource of RNA 3D structure benchmark datasets, structure manipulation, and evaluation tools (2019, background): “Most importantly, the RNA secondary structure, determined by the set of cis-Watson-Crick base pairs, can be generally determined using sequence comparisons (8, 9) However, the formation of a 3D structure requires, in addition, non-Watson-Crick base pairs (10), structural modules (11), and som”