ArticleJournal of computational chemistry2016
Additive CHARMM force field for naturally occurring modified ribonucleotides.
Article in Journal of computational chemistry, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 47 papers.
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Who cites it
47 citing papers in PubMed.
- Mechanistic studies on HNRNPA2B1 suggest binding but not selective recognition of mRNA biology · 2026Article
- Drude SILCS-Nucleic: harnessing explicit electronic polarization in targeting RNA and DNA for drug design.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
- RBM45 Preferential Binding to mThe journal of physical chemistry. B · 2026Article
- Structure-Based Simulations for Folding of a tRNA Isodecoder.Molecules (Basel, Switzerland) · 2026Article
- In silico aptamer design: from sequence selection to structural optimization and computational modelling strategies.Journal of computer-aided molecular design · 2026Review
- RNA binding protein Musashi1 interacts with the viral genomic RNA and restricts SARS-CoV-2 infection by repressing translation.Nucleic acids research · 2026Article
- Decoding pH-Driven Phase Transition of Lipid Nanoparticles.Small (Weinheim an der Bergstrasse, Germany) · 2026Article
- Drude SILCS-Nucleic: Harnessing Explicit Electronic Polarization in Targeting RNA and DNA for Drug Design.bioRxiv : the preprint server for biology · 2025Article
- Buffer optimization of siRNA-lipid nanoparticles mitigates lipid oxidation and RNA-lipid adduct formation.Nature communications · 2025Article
- Accurate in silico predictions of modified RNA interactions to a prototypical RNA-binding protein with λ-dynamics.RNA (New York, N.Y.) · 2025Article
- Increasing the Accuracy and Robustness of the CHARMM General Force Field with an Expanded Training Set.Journal of chemical theory and computation · 2025Article
- In silico λ-dynamics predicts protein binding specificities to modified RNAs.Nucleic acids research · 2025Article
- CHARMM at 45: Enhancements in Accessibility, Functionality, and Speed.The journal of physical chemistry. B · 2024Review
- Molecular Dynamics Simulation of Lipid Nanoparticles Encapsulating mRNA.Molecules (Basel, Switzerland) · 2024Article
- Employing Metadynamics to Predict the Membrane Partitioning of Carboxy-2The journal of physical chemistry. B · 2024Article
- Adenine Methylation Enhances the Conformational Flexibility of an RNA Hairpin Tetraloop.The journal of physical chemistry. B · 2024Article
- In silico λ-dynamics predicts protein binding specificities to modified RNAs.bioRxiv : the preprint server for biology · 2024Article
- CHARMM-GUI PDB Manipulator: Various PDB Structural Modifications for Biomolecular Modeling and Simulation.Journal of molecular biology · 2023Article
Corrections and comments
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Authors and funding
5 authors.
Funding
Abstract
More than 100 naturally occurring modified nucleotides have been found in RNA molecules, in particular in tRNAs. We have determined molecular mechanics force field parameters compatible with the CHARMM36 all-atom additive force field for all these modifications using the CHARMM force field parametrization strategy. Emphasis was placed on fine tuning of the partial atomic charges and torsion angle parameters. Quantum mechanics calculations on model compounds provided the initial set of target data, and extensive molecular dynamics simulations of nucleotides and oligonucleotides in aqueous solutions were used for further refinement against experimental data. The presented parameters will allow for computational studies of a wide range of RNAs containing modified nucleotides, including the ribosome and transfer RNAs.
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