Accurate SHAPE-directed RNA secondary structure modeling, including pseudoknots
By Christine E. Hajdin, Stanislav Bellaousov, Wayne Huggins, Christopher W. Leonard, D. Mathews, Kevin M. Weeks. Proceedings of the National Academy of Sciences of the United States of America, 2013
320 citations recorded by the source corpus.
Subfields: Molecular Biology
View Paper: https://www.semanticscholar.org/paper/6fb2d5fd011e3c89fa280a51adac3bcf2ebca00d
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In Molecular Biology
- Rhiju Das
- Janusz M. Bujnicki
- N. V. Dokholyan
- Eric Westhof
- Wipapat Kladwang
- Fang-Chieh Chou
- Marta Szachniuk
- Maciej Antczak
Citations in the corpus
- RNA-Puzzles Round II: assessment of RNA structure prediction programs applied to three large RNA structures (2015, methodology): “More recent versions of RNAstructure have updated parameters for nearest-neighbor energies and for converting SHAPE values to pseudoenergies, and also have the ability to model pseudoknots (Hajdin et al. 2013).”
- Pervasive tertiary structure in the dengue virus RNA genome (2018, methodology): “The MFE secondary structure (inverted black arcs) was obtained using both 1M7 and differential SHAPE reactivities as constraints (6, 9).”
- RNA motif discovery by SHAPE and mutational profiling (SHAPE-MaP) (2014, unknown): “These innovations include improved energy models, the ability to model pseudoknots, and concise strategies for detecting tertiary and noncanonical interactions 19,22 .”
- Modeling complex RNA tertiary folds with Rosetta. (2015, methodology): “…alignment, or targeting of “alternative” states of the RNA (e.g., without ligands or in misfolded conformations), chemicalmapping techniques provide useful guides to computational secondary structure prediction (Cordero, Kladwang, VanLang, & Das, 2014; Hajdin et al., 2013; Kladwang et al., 2011).”
- RNA-Puzzles Round III: 3D RNA structure prediction of five riboswitches and one ribozyme (2017, methodology): “Despite using the incorrect ligand, significant changes in SHAPE reactivity were observed as a function of Ni2+. SHAPEMaP-directed modeling (Siegfried et al. 2014) using ShapeKnots (Hajdin et al. 2013) resulted in a structure with a correctly predicted pseudoknot and with overall sensitivity and pos”
- RNA Secondary Structure Prediction By Learning Unrolled Algorithms (2020, background): “Pseudoknots make up roughly 1.4% of base-pairs (Mathews & Turner, 2006), and are overrepresented in functionally important regions (Hajdin et al., 2013; Staple & Butcher, 2005).”