ArticleBiopolymers2013
Twenty-five years of nucleic acid simulations.
Article in Biopolymers, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 86 papers.
What it found
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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
86 citing papers in PubMed.
- Toward Accurate RNA Folding Thermodynamics: Evaluation of Enhanced Sampling Methods for Force Field Benchmarking.Journal of chemical theory and computation · 2026Article
- Orchestrated metal ion repositioning defines the dynamic catalytic strategy of the essential DNA repair nuclease APE1.bioRxiv : the preprint server for biology · 2026Article
- Structural Dynamics of Peptiplexes Formed between Cationic Cell-Penetrating Peptides and DNA: A Comparative Study on TAT-HIV and NLS-SV40T.ACS applied bio materials · 2026Article
- Computer Simulations of Multidrug Efflux Pumps of the Resistance-Nodulation-Cell Division Superfamily.Methods in molecular biology (Clifton, N.J.) · 2026Article
- Integrating Magnetic Bead-Based SELEX withACS omega · 2025Article
- Decoding the base flipping mechanism of the SET- and RING-associated (SRA) domain of the epigenetic UHRF1 protein.Nucleic acids research · 2025Article
- Computer-Aided Discovery of Natural Compounds Targeting the ADAR2 dsRBD2-RNA Interface and Computational Modeling of Full-Length ADAR2 Protein Structure.International journal of molecular sciences · 2025Article
- Rational design yields RNA-binding zinc finger domains with altered sequence specificity.RNA (New York, N.Y.) · 2025Article
- MDTAP: a tool to analyze permeation events across membrane proteins.Bioinformatics advances · 2025Article
- Cleavage of DNA Substrate Containing Nucleotide Mismatch in the Complementary Region to sgRNA by Cas9 Endonuclease: Thermodynamic and Structural Features.International journal of molecular sciences · 2024Article
- Modeling allosteric mechanisms of eukaryotic type II topoisomerases.Biophysical journal · 2024Article
- Structural and Dynamic Features of the Recognition of 8-oxoguanosine Paired with an 8-oxoG-clamp by Human 8-oxoguanine-DNA Glycosylase.Current issues in molecular biology · 2024Article
- Rational Approach to Optimizing Conformation-Switching Aptamers for Biosensing Applications.ACS sensors · 2024Article
- Simple Adjustment of Intranucleotide Base-Phosphate Interaction in the OL3 AMBER Force Field Improves RNA Simulations.Journal of chemical theory and computation · 2023Article
- AmberTools.Journal of chemical information and modeling · 2023Article
- The effects of RNA.DNA-DNA triple helices on nucleosome structures and dynamics.Biophysical journal · 2023Article
- All-Atom Molecular Dynamics Simulations of Membrane-Spanning DNA Origami Nanopores.Methods in molecular biology (Clifton, N.J.) · 2023Article
- Structure- and Content-Dependent Efficiency of Cas9-Assisted DNA Cleavage in Genome-Editing Systems.International journal of molecular sciences · 2022Article
- Thermodynamic Swings: How Ideal Complex of Cas9-RNA/DNA Forms.International journal of molecular sciences · 2022Article
- Loading of DOX into a tetrahedral DNA nanostructure: the corner does matter.Nanoscale advances · 2022Article
26 more citing papers are in PubMed but not listed here.
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Authors and funding
2 authors.
Funding
Abstract
We present a brief, and largely personal, history of computer simulations of DNA and RNA oligonucleotides, with an emphasis on duplex structures and the Amber force fields. Both explicit and implicit solvent models are described, and methods for estimating structures, thermodynamics and mechanical properties of duplexes are illustrated. This overview, covering about two decades of work, provides a perspective for a discussion of prospects and obstacles for future simulations of RNA and DNA.
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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.