ReviewBiopolymers2007
Molecular dynamics simulations of RNA: an in silico single molecule approach.
Review in Biopolymers, 2007. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 57 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
57 citing papers in PubMed.
- Phase Separation of SARS-CoV-2 Nucleocapsid Protein with TDP-43 Is Dependent on C-Terminus Domains.International journal of molecular sciences · 2024Article
- Computer-Assisted Design and Characterization of RNA Nanostructures.Methods in molecular biology (Clifton, N.J.) · 2023Article
- Article
- Protein Interaction with Charged Macromolecules: From Model Polymers to Unfolded Proteins and Post-Translational Modifications.International journal of molecular sciences · 2019Review
- RNA Structural Differentiation: Opportunities with Pattern Recognition.Biochemistry · 2019Review
- Atomistic Analysis of ToxN and ToxI Complex Unbinding Mechanism.International journal of molecular sciences · 2018Article
- Review
- Effect of single-residue bulges on RNA double-helical structures: crystallographic database analysis and molecular dynamics simulation studies.Journal of molecular modeling · 2017Article
- Wobble pairs of the HDV ribozyme play specific roles in stabilization of active site dynamics.Physical chemistry chemical physics : PCCP · 2015Article
- Prediction of solution properties and dynamics of RNAs by means of Brownian dynamics simulation of coarse-grained models: Ribosomal 5S RNA and phenylalanine transfer RNA.BMC biophysics · 2015Article
- Multiscale methods for computational RNA enzymology.Methods in enzymology · 2015Article
- The purine riboswitch as a model system for exploring RNA biology and chemistry.Biochimica et biophysica acta · 2014Review
- Dynamics of riboswitches: Molecular simulations.Biochimica et biophysica acta · 2014Review
- Cooperative gene regulation by microRNA pairs and their identification using a computational workflow.Nucleic acids research · 2014Article
- Disparate HDV ribozyme crystal structures represent intermediates on a rugged free-energy landscape.RNA (New York, N.Y.) · 2014Article
- Nucleic acid catalysis: metals, nucleobases, and other cofactors.Chemical reviews · 2014Review
- Single molecule fluorescence approaches shed light on intracellular RNAs.Chemical reviews · 2014Review
- Interconversion between parallel and antiparallel conformations of a 4H RNA junction in domain 3 of foot-and-mouth disease virus IRES captured by dynamics simulations.Biophysical journal · 2014Article
- Multidimensional Replica Exchange Molecular Dynamics Yields a Converged Ensemble of an RNA Tetranucleotide.Journal of chemical theory and computation · 2014Article
- Classical electrostatics for biomolecular simulations.Chemical reviews · 2014Review
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
4 authors.
Funding
Abstract
RNA molecules are now known to be involved in the processing of genetic information at all levels, taking on a wide variety of central roles in the cell. Understanding how RNA molecules carry out their biological functions will require an understanding of structure and dynamics at the atomistic level, which can be significantly improved by combining computational simulation with experiment. This review provides a critical survey of the state of molecular dynamics (MD) simulations of RNA, including a discussion of important current limitations of the technique and examples of its successful application. Several types of simulations are discussed in detail, including those of structured RNA molecules and their interactions with the surrounding solvent and ions, catalytic RNAs, and RNA-small molecule and RNA-protein complexes. Increased cooperation between theorists and experimentalists will allow expanded judicious use of MD simulations to complement conceptually related single molecule experiments. Such cooperation will open the door to a fundamental understanding of the structure-function relationships in diverse and complex RNA molecules. .
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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.