Instituut-Lorentz for Theoretical Physics, Leiden University, P.O. Box 9506, 2300 RA Leiden, The Netherlands.
Institut de Mathématiques, Station 8, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne CH-1015, Switzerland.
Nucleic Acids Res. 2018 Jul 2;46(W1):W5-W10. doi: 10.1093/nar/gky351.
The sequence-dependent statistical mechanical properties of fragments of double-stranded DNA is believed to be pertinent to its biological function at length scales from a few base pairs (or bp) to a few hundreds of bp, e.g. indirect read-out protein binding sites, nucleosome positioning sequences, phased A-tracts, etc. In turn, the equilibrium statistical mechanics behaviour of DNA depends upon its ground state configuration, or minimum free energy shape, as well as on its fluctuations as governed by its stiffness (in an appropriate sense). We here present cgDNAweb, which provides browser-based interactive visualization of the sequence-dependent ground states of double-stranded DNA molecules, as predicted by the underlying cgDNA coarse-grain rigid-base model of fragments with arbitrary sequence. The cgDNAweb interface is specifically designed to facilitate comparison between ground state shapes of different sequences. The server is freely available at cgDNAweb.epfl.ch with no login requirement.
双链 DNA 片段的序列依赖性统计力学性质被认为与其生物学功能有关，其长度范围从几个碱基对（bp）到几百个 bp，例如间接读取蛋白结合位点、核小体定位序列、相 A 链段等。反过来，DNA 的平衡统计力学行为取决于其基态构型或最小自由能形状，以及由其刚度（在适当意义上）控制的波动。我们在这里提出了 cgDNAweb，它提供了基于浏览器的双链 DNA 分子序列依赖性基态的交互式可视化，这是由具有任意序列的 cgDNA 粗粒度刚性碱基模型预测的。cgDNAweb 界面专门设计用于促进不同序列的基态形状之间的比较。该服务器可在 cgDNAweb.epfl.ch 上免费使用，无需登录。
