ReviewFrontiers in molecular biosciences2021
Bottom-Up Coarse-Grained Modeling of DNA.
Review in Frontiers in molecular biosciences, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 17 papers.
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17 citing papers in PubMed.
- Recent advances in coarse-grained simulations of nucleic acid condensation.The Biochemical journal · 2026Review
- Active subspace learning for coarse-grained molecular dynamics.The Journal of chemical physics · 2026Article
- Abundant positively-charged proteins underlie JCVI-Syn3A's expanded nucleoid and ribosome distribution.PLoS computational biology · 2026Article
- The effects of DMSO on DNA conformations and mechanics.Biophysical journal · 2025Article
- Kinetics and dynamics of oligonucleotide hybridization.Nature reviews. Chemistry · 2025Review
- Toward Predictive Coarse-Grained Simulations of Biomolecular Condensates.Biochemistry · 2025Review
- Chromatin structures from integrated AI and polymer physics model.PLoS computational biology · 2025Article
- Computational Methods for Modeling Lipid-Mediated Active Pharmaceutical Ingredient Delivery.Molecular pharmaceutics · 2025Review
- Multiscale modeling reveals the ion-mediated phase separation of nucleosome core particles.Biophysical journal · 2024Article
- Developing an Implicit Solvation Machine Learning Model for Molecular Simulations of Ionic Media.Journal of chemical theory and computation · 2024Article
- Computational Modeling of DNA 3D Structures: From Dynamics and Mechanics to Folding.Molecules (Basel, Switzerland) · 2023Review
- Atomistic Picture of Opening-Closing Dynamics of DNA Holliday Junction Obtained by Molecular Simulations.Journal of chemical information and modeling · 2023Article
- An associative memory Hamiltonian model for DNA and nucleosomes.PLoS computational biology · 2023Article
- Ab initio predictions for 3D structure and stability of single- and double-stranded DNAs in ion solutions.PLoS computational biology · 2022Article
- Single-molecule biophysics experimentsiScience · 2022Article
- Theory and Practice of Coarse-Grained Molecular Dynamics of Biologically Important Systems.Biomolecules · 2021Article
- A journey through mapping space: characterising the statistical and metric properties of reduced representations of macromolecules.The European physical journal. B · 2021Article
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6 authors.
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Abstract
Recent advances in methodology enable effective coarse-grained modeling of deoxyribonucleic acid (DNA) based on underlying atomistic force field simulations. The so-called bottom-up coarse-graining practice separates fast and slow dynamic processes in molecular systems by averaging out fast degrees of freedom represented by the underlying fine-grained model. The resulting effective potential of interaction includes the contribution from fast degrees of freedom effectively in the form of potential of mean force. The pair-wise additive potential is usually adopted to construct the coarse-grained Hamiltonian for its efficiency in a computer simulation. In this review, we present a few well-developed bottom-up coarse-graining methods, discussing their application in modeling DNA properties such as DNA flexibility (persistence length), conformation, "melting," and DNA condensation.
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