ArticleNucleic acids research2014
cgDNA: a software package for the prediction of sequence-dependent coarse-grain free energies of B-form DNA.
Article in Nucleic acids research, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 24 papers.
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Who cites it
24 citing papers in PubMed.
- hexABC seeking the physical code of DNA.Nature communications · 2026Article
- cgNA+min: computation of sequence-dependent dsDNA energy-minimizing minicircles.Nucleic acids research · 2026Article
- Inferring DNA Kinkability from Biased MD Simulations.Journal of chemical theory and computation · 2026Article
- Nucleosome wrapping energy in CpG islands and the role of epigenetic base modifications.eLife · 2025Article
- Sequence-Dependent Shape and Stiffness of DNA and RNA Double Helices: Hexanucleotide Scale and Beyond.Journal of chemical information and modeling · 2025Article
- Laplace approximation of J factors for rigid base and rigid basepair models of DNA cyclization.Biophysical journal · 2025Article
- CGeNArate: a sequence-dependent coarse-grained model of DNA for accurate atomistic MD simulations of kb-long duplexes.Nucleic acids research · 2024Article
- Temperature-dependent elasticity of DNA, RNA, and hybrid double helices.Biophysical journal · 2024Article
- DNA supercoiling in bacteria: state of play and challenges from a viewpoint of physics based modeling.Frontiers in microbiology · 2023Review
- Accurate Sequence-Dependent Coarse-Grained Model for Conformational and Elastic Properties of Double-Stranded DNA.Journal of chemical theory and computation · 2022Article
- Contrast variation SAXS: Sample preparation protocols, experimental procedures, and data analysis.Methods in enzymology · 2022Article
- Sequence-dependent structural properties of B-DNA: what have we learned in 40 years?Biophysical reviews · 2021Review
- Ensembles of Breathing Nucleosomes: A Computational Study.Biophysical journal · 2020Article
- Genome Dashboards: Framework and Examples.Biophysical journal · 2020Article
- Structure-mechanics statistical learning unravels the linkage between local rigidity and global flexibility in nucleic acids.Chemical science · 2020Article
- A multi-modal coarse grained model of DNA flexibility mappable to the atomistic level.Nucleic acids research · 2020Article
- The static and dynamic structural heterogeneities of B-DNA: extending Calladine-Dickerson rules.Nucleic acids research · 2019Article
- Local DNA Sequence Controls Asymmetry of DNA Unwrapping from Nucleosome Core Particles.Biophysical journal · 2018Article
- cgDNAweb: a web interface to the cgDNA sequence-dependent coarse-grain model of double-stranded DNA.Nucleic acids research · 2018Article
- Quantifying the impact of simple DNA parameters on the cyclization J-factor for single-basepair-addition families.Scientific reports · 2018Article
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4 authors.
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Abstract
cgDNA is a package for the prediction of sequence-dependent configuration-space free energies for B-form DNA at the coarse-grain level of rigid bases. For a fragment of any given length and sequence, cgDNA calculates the configuration of the associated free energy minimizer, i.e. the relative positions and orientations of each base, along with a stiffness matrix, which together govern differences in free energies. The model predicts non-local (i.e. beyond base-pair step) sequence dependence of the free energy minimizer. Configurations can be input or output in either the Curves+ definition of the usual helical DNA structural variables, or as a PDB file of coordinates of base atoms. We illustrate the cgDNA package by comparing predictions of free energy minimizers from (a) the cgDNA model, (b) time-averaged atomistic molecular dynamics (or MD) simulations, and (c) NMR or X-ray experimental observation, for (i) the Dickerson-Drew dodecamer and (ii) three oligomers containing A-tracts. The cgDNA predictions are rather close to those of the MD simulations, but many orders of magnitude faster to compute. Both the cgDNA and MD predictions are in reasonable agreement with the available experimental data. Our conclusion is that cgDNA can serve as a highly efficient tool for studying structural variations in B-form DNA over a wide range of sequences.
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