ArticleJournal of chemical theory and computation2013
Toward Improved Description of DNA Backbone: Revisiting Epsilon and Zeta Torsion Force Field Parameters.
Article in Journal of chemical theory and computation, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 113 papers.
What it found
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Who cites it
113 citing papers in PubMed.
- Modeling conformational transitions in DNA, RNA, and protein-nucleic acid complexes.Nucleic acids research · 2026Article
- Programmable kinetic barcoding for multiplexed RNA detection with Cas13a.Nature biomedical engineering · 2026Article
- Critical structural perturbations of ribozyme active sites induced by 2'-O-methylation commonly used in structural studies.Nucleic acids research · 2026Article
- Interaction of Carbon Dots with Nucleic Acids Is Driven by Their Surface Charge.Journal of chemical information and modeling · 2026Article
- The Role of Active Site Hydrophobic Interactions in Facilitating Catalysis in Human Terminal Deoxynucleotidyl Transferase.International journal of molecular sciences · 2025Article
- Structural basis of bis-quinolinium ligands binding to quadruplex-duplex hybrids from PIM1 oncogene.Nucleic acids research · 2025Article
- Modeling Possible G-Quadruplexes and i-Motifs at DNA-DNA Contact Sites: Strategy, Classification, and Examples.International journal of molecular sciences · 2025Article
- DRLiPS: a novel method for prediction of druggable RNA-small molecule binding pockets using machine learning.Nucleic acids research · 2025Article
- Atomistic Insights Into Interaction of Doxorubicin With DNA: From Duplex to Nucleosome.Journal of computational chemistry · 2025Article
- Refinement of the Sugar Puckering Torsion Potential in the AMBER DNA Force Field.Journal of chemical theory and computation · 2025Article
- Unveiling the unusual i-motif-derived architecture of a DNA aptamer exhibiting high affinity for influenza A virus.Nucleic acids research · 2025Article
- Computer Folding of Parallel DNA G-Quadruplex: Hitchhiker's Guide to the Conformational Space.Journal of computational chemistry · 2025Article
- Complex Biophysical and Computational Analyses of G-Quadruplex Ligands: The Porphyrin Stacks Back.Chemistry (Weinheim an der Bergstrasse, Germany) · 2024Article
- modXNA: A Modular Approach to Parametrization of Modified Nucleic Acids for Use with Amber Force Fields.Journal of chemical theory and computation · 2024Article
- Mechanical Stability and Unfolding Pathways of Parallel Tetrameric G-Quadruplexes Probed by Pulling Simulations.Journal of chemical information and modeling · 2024Article
- van der Waals Parameter Scanning with Amber Nucleic Acid Force Fields: Revisiting Means to Better Capture the RNA/DNA Structure through MD.Journal of chemical theory and computation · 2024Article
- WhiA transcription factor provides feedback loop between translation and energy production in a genome-reduced bacterium.Frontiers in microbiology · 2024Article
- Insight into Tetramolecular DNA G-Quadruplexes Associated with ALS and FTLD: Cation Interactions and Formation of Higher-Ordered Structure.International journal of molecular sciences · 2023Article
- The development of nucleic acids force fields: From an unchallenged past to a competitive future.Biophysical journal · 2023Review
- Assessing the Current State of Amber Force Field Modifications for DNA─2023 Edition.Journal of chemical theory and computation · 2023Article
53 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
6 authors.
Funding
Abstract
We present a refinement of the backbone torsion parameters ε and ζ of the Cornell et al. AMBER force field for DNA simulations. The new parameters, denoted as εζ
Identifiers
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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 OpenQuestion graph.