ArticleJournal of chemical theory and computation2023
Assessing the Current State of Amber Force Field Modifications for DNA─2023 Edition.
Article in Journal of chemical theory and computation, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 29 papers.
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Who cites it
29 citing papers in PubMed.
- Recent advances in coarse-grained simulations of nucleic acid condensation.The Biochemical journal · 2026Review
- Dibenzoacridinium derivatives: a new class of G-quadruplex ligands with anti-HIV-1 properties.RSC medicinal chemistry · 2026Article
- Conformational analysis of nucleic acids for optimizing DNA and RNA topological models.Nucleic acids research · 2026Article
- Are we there yet with XNA aptamers?RSC advances · 2026Review
- 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
- Inferring DNA Kinkability from Biased MD Simulations.Journal of chemical theory and computation · 2026Article
- Interaction of Carbon Dots with Nucleic Acids Is Driven by Their Surface Charge.Journal of chemical information and modeling · 2026Article
- Computer Simulations of Multidrug Efflux Pumps of the Resistance-Nodulation-Cell Division Superfamily.Methods in molecular biology (Clifton, N.J.) · 2026Article
- Conformational changes induced by K949A mutation in the CRISPR-Cas12a complex drives an effective target-binding mechanism.Current research in structural biology · 2025Article
- Helical aromatic oligoamide foldamers as selective G-quadruplex ligands.Nucleic acids research · 2025Article
- Sequence-Dependent Shape and Stiffness of DNA and RNA Double Helices: Hexanucleotide Scale and Beyond.Journal of chemical information and modeling · 2025Article
- Coordinated Residue Motions at the Enzyme-Substrate Interface Promote DNA Translocation in Polymerases.Journal of the American Chemical Society · 2025Article
- Kinetics and dynamics of oligonucleotide hybridization.Nature reviews. Chemistry · 2025Review
- Mechanisms of DNA Damage Recognition by UDG and PARP1 in the Nucleosome.Biomolecules · 2025Article
- Computational Methods for Modeling Lipid-Mediated Active Pharmaceutical Ingredient Delivery.Molecular pharmaceutics · 2025Review
- Unveiling nucleosome dynamics: A comparative study using all-atom and coarse-grained simulations enhanced by principal component analysis.The Journal of chemical physics · 2025Article
- Refinement of the Sugar Puckering Torsion Potential in the AMBER DNA Force Field.Journal of chemical theory and computation · 2025Article
- Structural insights into the DNA-binding mechanism of BCL11A: The integral role of ZnF6.Structure (London, England : 1993) · 2024Article
- Comparative molecular dynamics calculations of duplexation of chemically modified analogs of DNA used for antisense applications.NAR genomics and bioinformatics · 2024Article
- Identifying the minimal sets of distance restraints for FRET-assisted protein structural modeling.Protein science : a publication of the Protein Society · 2024Article
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6 authors.
Funding
Abstract
Advances in molecular dynamics (MD) software alongside enhanced computational power and hardware have allowed for MD simulations to significantly expand our knowledge of biomolecular structure, dynamics, and interactions. Furthermore, it has allowed for the extension of conformational sampling times from nanoseconds to the microsecond level and beyond. This has not only made convergence of conformational ensembles through comprehensive sampling possible but consequently exposed deficiencies and allowed the community to overcome limitations in the available force fields. The reproducibility and accuracy of the force fields are imperative in order to produce biologically relevant data. The Amber nucleic acid force fields have been used widely since the mid-1980s, and improvement of these force fields has been a community effort with several artifacts revealed, corrected, and reevaluated by various research groups. Here, we focus on the Amber force fields for use with double-stranded DNA and present the assessment of two recently developed force field parameter sets (OL21 and Tumuc1). Extensive MD simulations were performed with six test systems and two different water models. We observe the improvement of OL21 and Tumuc1 compared to previous generations of the Amber DNA force. We did not detect any significant improvement in the performance of Tumuc1 compared to OL21 despite the reparameterization of bonded force field terms in the former; however, we did note discrepancies in Tumuc1 when modeling Z-DNA sequences.
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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 Socratic graph.