iFoldRNA v2: folding RNA with constraints

By Andrey Krokhotin, Kevin Houlihan, N. V. Dokholyan. 2015

102 citations recorded by the source corpus.

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In Molecular Biology

Citations in the corpus

RNA-Puzzles Round IV: 3D structure predictions of four ribozymes and two aptamers (2020, background): “According to the scaffold analysis (Porter et al. 2017), the secondary structure of 5-hydroxytryptophan riboswitch is similar to the guanine riboswitch (Batey et al. 2004), di-GMP riboswitch (Kulshina et al. 2009), and hammerhead ribozyme (Anderson et al. 2013), which have been reported.”
RNA-Puzzles Round III: 3D RNA structure prediction of five riboswitches and one ribozyme (2017, methodology): “The structure of the YbxF protein was predicted by fold-recognition using the GeneSilico metaserver (Kurowski and Bujnicki 2003), followed by template-based modeling using the L7Ae protein structure (PDB ID: 2FC3) as a template, with MODELLER (Sali and Blundell 1993).”
Pairing a high-resolution statistical potential with a nucleobase-centric sampling algorithm for improving RNA model refinement (2021, unknown): “Examples are FARNA 7 , MC-fold/MC-Sym 8 , Rosetta-SWM 9 , ifoldRNA 10,11 , Vfold 12,13 , 3dRNA 14,15 , and SimRNA 16 .”
FARFAR2: Improved de novo Rosetta prediction of complex global RNA folds (2020, unknown): “, 2017] and iFoldRNA [Krokhotin et al., 2015]), Monte Carlo (Rosetta FARFAR [Das and Baker, 2007] and SimRNA [Boniecki et al.”
CAMEO - Perspectives on the future of fully automated evaluation of structure prediction methods (2021, unknown): “Although several standalone approaches have been developed, 32,33 and fully automated web prediction servers 34 – 37 are available, predicting the 3D structure of nucleic acids, RNA in particular, remains a challenge and an area of active development.”