Tools for the automatic identification and classification of RNA base pairs

By Huanwang Yang, F. Jossinet, Neocles Leontis, Li Chen, John D. Westbrook, Helen M. Berman, Eric Westhof. Nucleic Acids Res., 2003

327 citations recorded by the source corpus.

Subfields: Materials Chemistry, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/0bd1a46abb024c00100afe1176bd6ca3ffbd073f

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Citations in the corpus

SimRNA: a coarse-grained method for RNA folding simulations and 3D structure prediction (2015, methodology): “For all sequences in the benchmark sets, we carried out tertiary structure prediction by de novo folding with SimRNA (folding using sequence alone) as well as folding with restraints on the secondary structure, obtained from the target structures using RNAView (36).”
CASP15 cryoEM protein and RNA targets: refinement and analysis using experimental maps (2023, methodology): “These subunits were composed of interacting secondary structure elements determined using DSSP 19 for proteins and RNAView 20 for RNA.”
Automated 3D structure composition for large RNAs (2012, methodology): “Base pair interactions and the base stacking network for the tertiary structures were obtained using RNAView (34) and MC-Annotate (35) programs, respectively.”
FR3D: finding local and composite recurrent structural motifs in RNA 3D structures (2007, methodology): “introduced three programs, BPViewer, RNAView, and RNAMLView, to aid in the classification and visualization of RNA structure [45].”
New metrics for comparing and assessing discrepancies between RNA 3D structures and models. (2009, methodology): “For practical reasons, we use two automated annotation procedures that have been proposed recently: MC-Annotate (Gendron et al. 2001; Lemieux and Major 2002) and RNAview (Yang et al. 2003).”
RNA-Puzzles: a CASP-like evaluation of RNA three-dimensional structure prediction. (2012, methodology): “The interaction (in magenta) was detected with the RNAView (Yang et al. 2003) annotation program but not with MC-Annotated (Gendron et al.”
bpRNA: large-scale automated annotation and analysis of RNA secondary structure (2018, methodology): “We first parsed the 3D structures from PDB files with the June 2017 version of RNAview(34), and used custom perl scripts to convert to BPSEQ format.”
ModeRNA: a tool for comparative modeling of RNA 3D structure (2011, methodology): “Instead, a manual alignment was generated with RNAView (50), aided by comparison of secondary structures.”
DSSR: an integrated software tool for dissecting the spatial structure of RNA (2015, background): “Existing RNA bioinformatics tools (Lemieux and Major, 2002; Yang et al., 2003; Sarver et al., 2008) are fragmented, and suffer in either scope or usability.”
ClaRNA: a classifier of contacts in RNA 3D structures based on a comparative analysis of various classification schemes (2014, methodology): “For assignment of pairwise interactions between ribonucleotides in RNA structures, the following third-party classifiers were used: MC-Annotate (5), RNAView (6) and FR3D (7).”