ArticleJournal of chemical theory and computation2018
AMOEBA Polarizable Atomic Multipole Force Field for Nucleic Acids.
Article in Journal of chemical theory and computation, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 119 papers.
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Who cites it
119 citing papers in PubMed.
- Drude SILCS-Nucleic: harnessing explicit electronic polarization in targeting RNA and DNA for drug design.Nucleic acids research · 2026Article
- Article
- Dual-LAO for calculating fast and robust relative binding free energies of simple and complex transformations.Communications chemistry · 2026Article
- A High-Throughput Platform for Rapid Adaptation of DNA Aptamers to SARS-CoV-2 Evolution.bioRxiv : the preprint server for biology · 2026Article
- A DNN Biophysics Model with Topological and Electrostatic Features.Journal of chemical information and modeling · 2026Article
- Investigating the electrostatics underlying activation of the βBiochimica et biophysica acta. Biomembranes · 2026Article
- Using experimental results of protein design to guide biomolecular energy-function development.PLoS computational biology · 2026Article
- Physical Confinement Modulates the Rate-Limiting Transition in the Release of Phosphate from Actin Filaments.bioRxiv : the preprint server for biology · 2026Article
- Graph-Based Deep Learning Models for Predicting pJournal of chemical information and modeling · 2026Article
- Capturing Carbohydrate Conformations and Hydration Interactions with a Polarizable Bond Dipole Potential.Molecules (Basel, Switzerland) · 2026Article
- Water Accelerates in the Hydration Shell of the N- and C-Terminal Domains of α-Synuclein in the Presence of NaCl.The journal of physical chemistry. B · 2026Article
- Critical structural perturbations of ribozyme active sites induced by 2'-O-methylation commonly used in structural studies.Nucleic acids research · 2026Article
- HessFit: Deriving Molecule-Specific Force Fields from Quantum Mechanical Hessians.Methods in molecular biology (Clifton, N.J.) · 2026Article
- Computational Ligand-Binding Site Prediction.Advances in experimental medicine and biology · 2026Review
- Molecular Simulation of Hydrogen Systems: From Properties and Methods to Applications and Future Directions.Chemical reviews · 2025Review
- The Kink-Turn 7 Motif: An Additional Test for RNA Force Field Performance.Journal of chemical theory and computation · 2025Article
- Drude SILCS-Nucleic: Harnessing Explicit Electronic Polarization in Targeting RNA and DNA for Drug Design.bioRxiv : the preprint server for biology · 2025Article
- Comparing Force Field Treatments in QM/MM Studies of the SARS-CoV-2 RNA-Dependent RNA Polymerase (RdRp) Mechanism.Journal of chemical theory and computation · 2025Article
- Targeting RNA with small molecules using state-of-the-art methods provides highly predictive affinities of riboswitch inhibitors.Communications biology · 2025Article
- Solvation Free Energies of Drug-like Molecules via Fast Growth in an Explicit Solvent: Assessment of the AM1-BCC, RESP/HF/6-31G*, RESP-QM/MM, and ABCG2 Fixed-Charge Approaches.Journal of chemical theory and computation · 2025Article
59 more citing papers are in PubMed but not listed here.
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Authors and funding
7 authors.
Funding
Abstract
The AMOEBA polarizable atomic multipole force field for nucleic acids is presented. Valence and electrostatic parameters were determined from high-level quantum mechanical data, including structures, conformational energy, and electrostatic potentials, of nucleotide model compounds. Previously derived parameters for the phosphate group and nucleobases were incorporated. A total of over 35 μs of condensed-phase molecular dynamics simulations of DNA and RNA molecules in aqueous solution and crystal lattice were performed to validate and refine the force field. The solution and/or crystal structures of DNA B-form duplexes, RNA duplexes, and hairpins were captured with an average root-mean-squared deviation from NMR structures below or around 2.0 Å. Structural details, such as base pairing and stacking, sugar puckering, backbone and χ-torsion angles, groove geometries, and crystal packing interfaces, agreed well with NMR and/or X-ray. The interconversion between A- and B-form DNAs was observed in ethanol-water mixtures at 328 K. Crystal lattices of B- and Z-form DNA and A-form RNA were examined with simulations. For the RNA tetraloop, single strand tetramers, and HIV TAR with 29 residues, the simulated conformational states,
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