ArticleThe Journal of chemical physics2011
A coarse-grain three-site-per-nucleotide model for DNA with explicit ions.
Article in The Journal of chemical physics, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 23 papers.
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Who cites it
23 citing papers in PubMed.
- Recent advances in coarse-grained simulations of nucleic acid condensation.The Biochemical journal · 2026Review
- NEAT-DNA: A Chemically Accurate, Sequence-Dependent Coarse-Grained Model for Large-Scale DNA Simulations.Journal of chemical theory and computation · 2026Article
- NEAT-DNA: A Chemically Accurate, Sequence-Dependent Coarse-Grained Model for Large-Scale DNA Simulations.bioRxiv : the preprint server for biology · 2025Article
- Ion-mediated effects of glycosylation on the disordered mucin domain: Insights from coarse-grained simulations.Biophysical journal · 2025Article
- 3D structure and stability prediction of DNA with multi-way junctions in ionic solutions.PLoS computational biology · 2025Article
- Connected Chromatin Amplifies Acetylation-Modulated Nucleosome Interactions.Biochemistry · 2025Article
- Article
- Explicit Ion Modeling Predicts Physicochemical Interactions for Chromatin Organization.bioRxiv : the preprint server for biology · 2023Article
- Investigating the Hydrogen Bond-Induced Self-Assembly of Polysulfamides Using Molecular Simulations and Experiments.Macromolecules · 2023Article
- Stability and Existence of Noncanonical I-motif DNA Structures in Computer Simulations Based on Atomistic and Coarse-Grained Force Fields.Molecules (Basel, Switzerland) · 2022Article
- Multiscale modeling of genome organization with maximum entropy optimization.The Journal of chemical physics · 2021Article
- Stability and folding pathways of tetra-nucleosome from six-dimensional free energy surface.Nature communications · 2021Article
- ssDNA diffuses along replication protein A via a reptation mechanism.Nucleic acids research · 2020Article
- Structure, stability and specificity of the binding of ssDNA and ssRNA with proteins.PLoS computational biology · 2019Article
- The Statistical Segment Length of DNA: Opportunities for Biomechanical Modeling in Polymer Physics and Next-Generation Genomics.Journal of biomechanical engineering · 2018Article
- Structural Characterization of Bubbles Formed in DNA Melting: A Monte Carlo Simulation Study.ACS omega · 2017Article
- The "sugar" coarse-grained DNA model.Journal of molecular modeling · 2017Article
- Molecular determinants of the interactions between proteins and ssDNA.Proceedings of the National Academy of Sciences of the United States of America · 2015Article
- Simple Elastic Network Models for Exhaustive Analysis of Long Double-Stranded DNA Dynamics with Sequence Geometry Dependence.PloS one · 2015Article
- Melting dynamics of short dsDNA chains in saline solutions.SpringerPlus · 2015Article
Corrections and comments
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Authors and funding
3 authors.
Funding
Abstract
The "three sites per nucleotide" (3SPN) model provides a coarse-grained representation of nucleic acids for simulation of molecular processes. Previously, this model has relied on an implicit representation of the surrounding ionic environment at the level of Debye-Hückel theory. In this work, we eliminate this limitation and present an explicit representation of ions, both monovalent and divalent. The coarse-grain ion-ion and ion-phosphate potential energy functions are inferred from all-atom simulations and parameterized to reproduce key features of the local structure and organization of ions in bulk water and in the presence of DNA. The resulting model, 3SPN.1-I, is capable of reproducing the local structure observed in detailed atomistic simulations, as well as the experimental melting temperature of DNA for a range of DNA oligonucleotide lengths, CG-content, Na(+) concentration, and Mg(2+) concentration.
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