An enumerative stepwise ansatz enables atomic-accuracy RNA loop modeling

By Parin Sripakdeevong, Wipapat Kladwang, Rhiju Das. 2011

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In Molecular Biology

Citations in the corpus

RNA Structure Refinement using the ERRASER-Phenix pipeline (2013, methodology): “Inspired by recent advances in ab initio RNA structure prediction (6-8) and successful applications of the Rosetta modeling suite in crystallographic and electron microscopy density fitting problems (9, 10), we recently developed the ERRASER method and coupled it with Phenix diffraction-based…”
Blind prediction of noncanonical RNA structure at atomic accuracy (2017, background): “conformations for each added nucleotide, could lead to atomic accuracy models of single stranded RNA loops (5).”
RNA-Puzzles: a CASP-like evaluation of RNA three-dimensional structure prediction. (2012, methodology): “There, it was possible to sample the crystallographic loop conformation but not to select it as the lowest-energy structure; the loop forms direct hydrogen bonds to metal ions, and these interactions are not yet modeled in Rosetta.”
Modeling complex RNA tertiary folds with Rosetta. (2015, methodology): “…landscape is too “rugged”; that is, it contains many energy minima that can trap the nascent model from exploring alternative conformations, and strategies for searching this landscape (Sripakdeevong et al., 2011) are currently too computationally expensive for RNA domains above 10–20 nucleotides.”
Chemical shift-based methods in NMR structure determination (2018, background): “More recently, two complementary approaches, FARFAR (Fragment Assembly of RNA with Full Atom Refinement) [208] and SWA (Stepwise Assembly) [209] have exhibited favorable outcomes in modeling non-canonical regions using realistic force fields.”
RNA-Puzzles Round II: assessment of RNA structure prediction programs applied to three large RNA structures (2015, background): “Finally, an expansion of “stepwise” assembly was piloted, previously developed for enumerative high-resolution modeling of motifs (Sripakdeevong et al. 2011; Chou et al. 2013), to gene rate complex RNA folds by progressively closing “rings” of motifs through numerous tertiary buildup paths (e.g.,…”