ArticlePloS one2013
Molecular dynamics simulations of double-stranded DNA in an explicit solvent model with the zero-dipole summation method.
Article in PloS one, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 8 papers.
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Who cites it
8 citing papers in PubMed, 25 citations in OpenAlex.
- Non-Ewald methods for evaluating the electrostatic interactions of charge systems: similarity and difference.Biophysical reviews · 2022Review
- Thermal stability of single-domain antibodies estimated by molecular dynamics simulations.Protein science : a publication of the Protein Society · 2019Article
- Phosphorylation of an intrinsically disordered region of Ets1 shifts a multi-modal interaction ensemble to an auto-inhibitory state.Nucleic acids research · 2018Article
- Molecular mechanisms of cooperative binding of transcription factors Runx1-CBFβ-Ets1 on the TCRα gene enhancer.PloS one · 2017Article
- Elastic properties of dynein motor domain obtained from all-atom molecular dynamics simulations.Protein engineering, design & selection : PEDS · 2016Article
- myPresto/omegagene: a GPU-accelerated molecular dynamics simulator tailored for enhanced conformational sampling methods with a non-Ewald electrostatic scheme.Biophysics and physicobiology · 2016Article
- Mathematical and computational modeling in biology at multiple scales.Theoretical biology & medical modelling · 2014Review
- A novel approach of dynamic cross correlation analysis on molecular dynamics simulations and its application to Ets1 dimer-DNA complex.PloS one · 2014Article
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4 authors at 1 institution in 1 country.
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No grant is acknowledged in the PubMed record.
Abstract
Molecular dynamics (MD) simulations of a double-stranded DNA with explicit water and small ions were performed with the zero-dipole summation (ZD) method, which was recently developed as one of the non-Ewald methods. Double-stranded DNA is highly charged and polar, with phosphate groups in its backbone and their counterions, and thus precise treatment for the long-range electrostatic interactions is always required to maintain the stable and native double-stranded form. A simple truncation method deforms it profoundly. On the contrary, the ZD method, which considers the neutralities of charges and dipoles in a truncated subset, well reproduced the electrostatic energies of the DNA system calculated by the Ewald method. The MD simulations using the ZD method provided a stable DNA system, with similar structures and dynamic properties to those produced by the conventional Particle mesh Ewald method.
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