ArticleNucleic acids research2024
SimRNAweb v2.0: a web server for RNA folding simulations and 3D structure modeling, with optional restraints and enhanced analysis of folding trajectories.
Article in Nucleic acids research, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. An erratum has been issued. Cited by 14 papers.
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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.
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Who cites it
14 citing papers in PubMed.
- RNAbpFlow: base pair-augmented SE(3) flow matching for conditional RNA 3D structure generation.Nature methods · 2026Article
- Prediction of Ligand Binding to Transthyretin Using Machine Learning Algorithms and Low-Dimensional Molecular Descriptors: A Tox24 Challenge Study.Chemical research in toxicology · 2026Article
- Recent Advances in Chemical Probing Strategies for RNA Structure Determination In Vivo.Chemistry (Weinheim an der Bergstrasse, Germany) · 2026Review
- ARNy plotter: A comprehensive web server for RNA ensemble structural analysis and visualization.PLoS computational biology · 2026Article
- TiRNA: a coarse-grained method with temperature and ion effects for RNA structure folding and prediction.Nucleic acids research · 2026Article
- Iron Regulatory Mechanism IRE/IRP-like in Two Protozoa of Importance to Human Health,Pathogens (Basel, Switzerland) · 2026Review
- DNATCO v5.0: integrated web platform for 3D nucleic acid structure analysis.Nucleic acids research · 2026Article
- Functional Relevance of CASP16 Nucleic Acid Predictions as Evaluated by Structure Providers.Proteins · 2026Article
- Solution structure determination and biophysical characterization studies of 7SK RNP and 7SL SRP RNAs.RNA (New York, N.Y.) · 2025Article
- RNA G-quadruplexes emerge from a compacted coil-like ensemble via multiple pathways.Nucleic acids research · 2025Article
- Structures and mechanisms of U6 snRNA mNature communications · 2025Article
- Functional relevance of CASP16 nucleic acid predictions as evaluated by structure providers.bioRxiv : the preprint server for biology · 2025Article
- DesiRNA: structure-based design of RNA sequences with a replica exchange Monte Carlo approach.Nucleic acids research · 2025Article
- Advances and Challenges in Scoring Functions for RNA-Protein Complex Structure Prediction.Biomolecules · 2024Review
Corrections and comments
- Erratum issued
Authors and funding
11 authors.
Funding
Abstract
Research on ribonucleic acid (RNA) structures and functions benefits from easy-to-use tools for computational prediction and analyses of RNA three-dimensional (3D) structure. The SimRNAweb server version 2.0 offers an enhanced, user-friendly platform for RNA 3D structure prediction and analysis of RNA folding trajectories based on the SimRNA method. SimRNA employs a coarse-grained model, Monte Carlo sampling and statistical potentials to explore RNA conformational space, optionally guided by spatial restraints. Recognized for its accuracy in RNA 3D structure prediction in RNA-Puzzles and CASP competitions, SimRNA is particularly useful for incorporating restraints based on experimental data. The new server version introduces performance optimizations and extends user control over simulations and the processing of results. It allows the application of various hard and soft restraints, accommodating alternative structures involving canonical and noncanonical base pairs and unpaired residues, while also integrating data from chemical probing methods. Enhanced features include an improved analysis of folding trajectories, offering advanced clustering options and multiple analyses of the generated trajectories. These updates provide comprehensive tools for detailed RNA structure analysis. SimRNAweb v2.0 significantly broadens the scope of RNA modeling, emphasizing flexibility and user-defined parameter control. The web server is available at https://genesilico.pl/SimRNAweb.
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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.