ArticleNucleic acids research2018
A nucleobase-centered coarse-grained representation for structure prediction of RNA motifs.
Article in Nucleic acids research, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 18 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
18 citing papers in PubMed.
- Ensemble refinement of mismodeled cryo-EM RNA structures using all-atom simulations.Nature communications · 2025Article
- Unknotting RNA: A method to resolve computational artifacts.PLoS computational biology · 2025Article
- RNA-Puzzles Round V: blind predictions of 23 RNA structures.Nature methods · 2025Article
- Sampling globally and locally correct RNA 3D structures using Ernwin, SPQR and experimental SAXS data.Nucleic acids research · 2024Article
- Machine learning in RNA structure prediction: Advances and challenges.Biophysical journal · 2024Review
- The Multiscale Ernwin/SPQR RNA Structure Prediction Pipeline.Methods in molecular biology (Clifton, N.J.) · 2024Article
- smFRET-assisted RNA structure prediction.Communications in information and systems · 2024Article
- RNA folding pathways from all-atom simulations with a variationally improved history-dependent bias.Biophysical journal · 2023Article
- RNAJP: enhanced RNA 3D structure predictions with non-canonical interactions and global topology sampling.Nucleic acids research · 2023Article
- Article
- Structural 3D Domain Reconstruction of the RNA Genome from Viruses with Secondary Structure Models.Viruses · 2021Article
- Pairing a high-resolution statistical potential with a nucleobase-centric sampling algorithm for improving RNA model refinement.Nature communications · 2021Article
- IsRNA1:Journal of chemical theory and computation · 2021Article
- RNA 3D Structure Prediction Using Coarse-Grained Models.Frontiers in molecular biosciences · 2021Review
- ToGo-WF: prediction of RNA tertiary structures and RNA-RNA/protein interactions using the KNIME workflow.Journal of computer-aided molecular design · 2019Article
- Barnaba: software for analysis of nucleic acid structures and trajectories.RNA (New York, N.Y.) · 2019Article
- Advances in coarse-grained modeling of macromolecular complexes.Current opinion in structural biology · 2018Review
- RNA Structural Dynamics As Captured by Molecular Simulations: A Comprehensive Overview.Chemical reviews · 2018Review
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
3 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
We introduce the SPlit-and-conQueR (SPQR) model, a coarse-grained (CG) representation of RNA designed for structure prediction and refinement. In our approach, the representation of a nucleotide consists of a point particle for the phosphate group and an anisotropic particle for the nucleoside. The interactions are, in principle, knowledge-based potentials inspired by the $\mathcal {E}$SCORE function, a base-centered scoring function. However, a special treatment is given to base-pairing interactions and certain geometrical conformations which are lost in a raw knowledge-based model. This results in a representation able to describe planar canonical and non-canonical base pairs and base-phosphate interactions and to distinguish sugar puckers and glycosidic torsion conformations. The model is applied to the folding of several structures, including duplexes with internal loops of non-canonical base pairs, tetraloops, junctions and a pseudoknot. For the majority of these systems, experimental structures are correctly predicted at the level of individual contacts. We also propose a method for efficiently reintroducing atomistic detail from the CG representation.
Indexed as
Identifiers
What OpenQuestion holds
Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.