cgNA+web : A Visual Interface to the cgNA+ Sequence-dependent Statistical Mechanics Model of Double-stranded Nucleic Acids
Journal of Molecular Biology, vol. 435, pp. 167978
Abstract
The sequence-dependent statistical mechanics of double-stranded nucleic acid, or dsNA, is believed to be essential in its biological functions. In turn, the equilibrium statistical mechanics behaviour of dsNA depends strongly both on sequence-dependent perturbations in its ground state shape away from an idealised, uniform, double-helical configuration, and on its fluctuations as governed by its sequence-dependent stiffness. We here describe the cgNA+web browser-based interactive tool for visualising the sequence-dependent ground states of dsNA fragments of arbitrary sequences, as predicted by the underlying cgNA+ coarse-grain model. Parameter sets are provided to model dsDNA, including the possibility of epigenetically modified CpG dinucleotide steps, dsRNA, and DNA:RNA Hybrid double helical fragments. The cgNA+web interface is specifically designed to compare ground state shapes of different sequences of the same dsNA, or analogous sequences of different dsNAs. The cgNA+web server is freely available at cgDNAweb.epfl.ch without any login requirement.
Authors 4
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École Polytechnique Fédérale de Lausanne
Affiliation as printed
Laboratory for Computation and Visualisation in Mathematics and Mechanics, Institute of Mathematics, École Polytechnique Fédérale de Lausanne, Lausanne 1015, Switzerland
Laboratory for Computation and Visualisation in Mathematics and Mechanics, Institute of Mathematics, École Polytechnique Fédérale de Lausanne, Lausanne, 1015, Switzerland
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École Polytechnique Fédérale de Lausanne
Affiliation as printed
Laboratory for Computation and Visualisation in Mathematics and Mechanics, Institute of Mathematics, École Polytechnique Fédérale de Lausanne, Lausanne 1015, Switzerland
Laboratory for Computation and Visualisation in Mathematics and Mechanics, Institute of Mathematics, École Polytechnique Fédérale de Lausanne, Lausanne, 1015, Switzerland
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Affiliation as printed
Institute Lorentz for Theoretical Physics, Leiden University, Leiden, The Netherlands
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École Polytechnique Fédérale de Lausanne
Affiliation as printed
Laboratory for Computation and Visualisation in Mathematics and Mechanics, Institute of Mathematics, École Polytechnique Fédérale de Lausanne, Lausanne 1015, Switzerland. Electronic address: john.maddocks@epfl.ch
Laboratory for Computation and Visualisation in Mathematics and Mechanics, Institute of Mathematics, École Polytechnique Fédérale de Lausanne, Lausanne, 1015, Switzerland
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