ArticleJournal of computational chemistry2011
Impact of 2'-hydroxyl sampling on the conformational properties of RNA: update of the CHARMM all-atom additive force field for RNA.
Article in Journal of computational chemistry, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 205 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
205 citing papers in PubMed.
- Recent advances in coarse-grained simulations of nucleic acid condensation.The Biochemical journal · 2026Review
- In silico designing of small molecules for targeting RNA: current landscape and future directions.Journal of computer-aided molecular design · 2026Review
- Modeling conformational transitions in DNA, RNA, and protein-nucleic acid complexes.Nucleic acids research · 2026Article
- Thermophysical Properties of a tRNA Isodecoder.The journal of physical chemistry. B · 2026Article
- The role of the 2'-OH group in phase separation and percolation transitions of RNA.Nature communications · 2026Article
- Unraveling the Mechanism of Drug Binding to SARS-CoV-2 RNA Pseudoknot With Thermodynamics-Driven Machine Learning.Journal of computational chemistry · 2026Article
- RBM45 Preferential Binding to mThe journal of physical chemistry. B · 2026Article
- Reparameterization of the Amber RNA Force Field Non-Bonded Terms.bioRxiv : the preprint server for biology · 2026Article
- Structure-Based Simulations for Folding of a tRNA Isodecoder.Molecules (Basel, Switzerland) · 2026Article
- Are we there yet with XNA aptamers?RSC advances · 2026Review
- Decoding pH-Driven Phase Transition of Lipid Nanoparticles.Small (Weinheim an der Bergstrasse, Germany) · 2026Article
- EXOSC3 G191 Variants Trigger System-Wide Recalibration of RNA Processing Machinery.bioRxiv : the preprint server for biology · 2026Article
- NMR and molecular dynamics demonstrate the RNA internal loop GAGU is dynamic and adjacent basepairs determine conformational preference.Biophysical journal · 2026Article
- The Kink-Turn 7 Motif: An Additional Test for RNA Force Field Performance.Journal of chemical theory and computation · 2025Article
- The C-terminal tails of GroEL and its mitochondrial and chloroplastic homologs adopt polyproline II helices.Protein science : a publication of the Protein Society · 2025Article
- Buffer optimization of siRNA-lipid nanoparticles mitigates lipid oxidation and RNA-lipid adduct formation.Nature communications · 2025Article
- Mechanistic Insights into SAM-Dependent Methyltransferases: A Review of Computational Approaches.International journal of molecular sciences · 2025Review
- Accurate in silico predictions of modified RNA interactions to a prototypical RNA-binding protein with λ-dynamics.RNA (New York, N.Y.) · 2025Article
- Mechanism for Nucleotidyl Transfer in LINE-1 ORF2p Revealed by QM/MM Simulations.International journal of molecular sciences · 2025Article
- Substrate Activation Efficiency in Active Sites of Hydrolases Determined by QM/MM Molecular Dynamics and Neural Networks.International journal of molecular sciences · 2025Article
145 more citing papers are in PubMed but not listed here.
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
Here, we present an update of the CHARMM27 all-atom additive force field for nucleic acids that improves the treatment of RNA molecules. The original CHARMM27 force field parameters exhibit enhanced Watson-Crick base pair opening which is not consistent with experiment, whereas analysis of molecular dynamics (MD) simulations show the 2'-hydroxyl moiety to almost exclusively sample the O3' orientation. Quantum mechanical (QM) studies of RNA related model compounds indicate the energy minimum associated with the O3' orientation to be too favorable, consistent with the MD results. Optimization of the dihedral parameters dictating the energy of the 2'-hydroxyl proton targeting the QM data yielded several parameter sets, which sample both the base and O3' orientations of the 2'-hydroxyl to varying degrees. Selection of the final dihedral parameters was based on reproduction of hydration behavior as related to a survey of crystallographic data and better agreement with experimental NMR J-coupling values. Application of the model, designated CHARMM36, to a collection of canonical and noncanonical RNA molecules reveals overall improved agreement with a range of experimental observables as compared to CHARMM27. The results also indicate the sensitivity of the conformational heterogeneity of RNA to the orientation of the 2'-hydroxyl moiety and support a model whereby the 2'-hydroxyl can enhance the probability of conformational transitions in RNA.
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.