Automated de novo prediction of native-like RNA tertiary structures

By Rhiju Das, David Baker. Proceedings of the National Academy of Sciences of the United States of America, 2007

460 citations recorded by the source corpus.

Subfields: Materials Chemistry, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/c442746c87b3a02fd1b250978b8a2da304aa4580

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In Materials Chemistry

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Citations in the corpus

RNA-Puzzles toolkit: a computational resource of RNA 3D structure benchmark datasets, structure manipulation, and evaluation tools (2019, methodology): “Second, the package contains scripts to help the RNA 3D structure prediction processes, both for SimRNA (42) (including SimRNAweb (58)), and Rosetta (59).”
SimRNA: a coarse-grained method for RNA folding simulations and 3D structure prediction (2015, methodology): “Thus far, various methods for RNA folding simulations have been developed, and they have used a variety of RNA structure representations, conformational sampling schemes and energy / scoring functions (8–12).”
FARFAR2: Improved de novo Rosetta prediction of complex global RNA folds (2020, unknown): “, 2015]), Monte Carlo (Rosetta FARFAR [Das and Baker, 2007] and SimRNA [Boniecki et al.”
3D RNA and Functional Interactions from Evolutionary Couplings. (2015, unknown): “Thus, despite rapid strides in 3D structure prediction accuracy for small (< 40 nt) RNAs (Cao and Chen, 2011; Das and Baker, 2007; Das et al., 2010; Frellsen et al., 2009; Parisien and Major, 2008), predicting the structure of large (> 70 nt) RNAs remains challenging (Laing and Schlick, 2010; Miao…”
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…”
An enumerative stepwise ansatz enables atomic-accuracy RNA loop modeling (2011, methodology): “There have been numerous recent successes in the highresolution modeling of small proteins (1–3), protein/RNA complexes (4), and protein/DNA interfaces (5) by optimizing physically realistic energy functions.”
Chemical shift-based methods in NMR structure determination (2018, methodology): “In particular, FARFAR employs a fragment assembly approach [204] to model low resolution structures following full-atom refinement using a high resolution energy function.”
Pairing a high-resolution statistical potential with a nucleobase-centric sampling algorithm for improving RNA model refinement (2021, unknown): “FARFAR 23,24 improves model accuracy through all-atom re ﬁ nement after FARNA coarse-grained sampling.”
Rosetta3: An Object-Oriented Software Suite for the Simulation and Design of Macromolecules (2011, unknown): “…of a set of protein loops (Mandell et al. , 2009; Rohl et al. , 2004) rna_denovo Predict the folded structure of an RNA molecule given its sequence (Das and Baker, 2007) rna_design Design a new sequence for an RNA molecule (Das et al. , 2010) that would have been virtually impossible in ROSETTA…”
New metrics for comparing and assessing discrepancies between RNA 3D structures and models. (2009, methodology): “Alternative methods include interactive modeling (Michel and Westhof 1990; Massire and Westhof 1998; Martinez et al. 2008) and conformational space searching (Das and Baker 2007; Ding et al. 2008; Parisien and Major 2008; Jonikas et al. 2009).”