ArticleNucleic acids research2008
Towards a molecular dynamics consensus view of B-DNA flexibility.
Article in Nucleic acids research, 2008. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 79 papers, 1 of them a synthesis that pooled it.
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Who cites it
79 citing papers in PubMed, 1 synthesis or guideline pooled it.
- An understanding of coronavirus and exploring the molecular dynamics simulations to find promising candidates against the Mpro of nCoV to combat the COVID-19: A systematic review.Journal of infection and public health · 2022Pooled it
- Impact of spatial lesion symmetry on the structural response of hydroxylated B-DNA.Scientific reports · 2025Article
- Sequence Dependence in Nucleosome Dynamics.The journal of physical chemistry. B · 2024Article
- Predicting DNA structure using a deep learning method.Nature communications · 2024Article
- Controlled sulfur-based engineering confers mouldability to phosphorothioate antisense oligonucleotides.Nucleic acids research · 2023Article
- Correlated motions in DNA: beyond base-pair step models of DNA flexibility.Nucleic acids research · 2023Article
- How acidic amino acid residues facilitate DNA target site selection.Proceedings of the National Academy of Sciences of the United States of America · 2023Article
- Pre-exascale HPC approaches for molecular dynamics simulations. Covid-19 research: A use case.Wiley interdisciplinary reviews. Computational molecular science · 2022Article
- Review on the QM/MM Methodologies and Their Application to Metalloproteins.Molecules (Basel, Switzerland) · 2022Review
- Computational investigation of the impact of core sequence on immobile DNA four-way junction structure and dynamics.Nucleic acids research · 2022Article
- Molecular basis of Arginine and Lysine DNA sequence-dependent thermo-stability modulation.PLoS computational biology · 2022Article
- Sequence-dependent structural properties of B-DNA: what have we learned in 40 years?Biophysical reviews · 2021Review
- Molecular mechanism of methyl-dependent and spatial-specific DNA recognition of c-Jun homodimer.Journal of molecular modeling · 2021Article
- Single-molecule micromanipulation studies of methylated DNA.Biophysical journal · 2021Article
- Spontaneous Embedding of DNA Mismatches Within the RNA:DNA Hybrid of CRISPR-Cas9.Frontiers in molecular biosciences · 2020Article
- Bending of DNA duplexes with mutation motifs.DNA research : an international journal for rapid publication of reports on genes and genomes · 2019Article
- Deciphering Off-Target Effects in CRISPR-Cas9 through Accelerated Molecular Dynamics.ACS central science · 2019Article
- Twist-bend coupling and the statistical mechanics of the twistable wormlike-chain model of DNA: Perturbation theory and beyond.Physical review. E · 2019Article
- Investigating the sequence-dependent mechanical properties of DNA nicks for applications in twisted DNA nanostructure design.Nucleic acids research · 2019Article
- Detailed Analysis of 17β-Estradiol-Aptamer Interactions: A Molecular Dynamics Simulation Study.Molecules (Basel, Switzerland) · 2018Article
19 more citing papers are in PubMed but not listed here.
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Authors and funding
4 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
We present a systematic study of B-DNA flexibility in aqueous solution using long-scale molecular dynamics simulations with the two more recent versions of nucleic acids force fields (CHARMM27 and parmbsc0) using four long duplexes designed to contain several copies of each individual base pair step. Our study highlights some differences between pambsc0 and CHARMM27 families of simulations, but also extensive agreement in the representation of DNA flexibility. We also performed additional simulations with the older AMBER force fields parm94 and parm99, corrected for non-canonical backbone flips. Taken together, the results allow us to draw for the first time a consensus molecular dynamics picture of B-DNA flexibility.
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