cgDNAweb is a web-based tool to interactively visualize the cgDNA tool predictions of the minimal free energy state of DNA double helices. The cgDNAweb can visualize the ground state configurations as 2D, 3D plots at several levels of detail.
Nucleic acid structure analysis; Data visualisation
De Bruin L, Maddocks JH "cgDNAweb: a web interface to the cgDNA sequence-dependent coarse-grain model of double-stranded DNA." Nucleic Acids Res. 2018; 46(W1):W5-W10 https://doi.org/10.1093/nar/gky351
PMID: 29905876
PMCID: PMC6030996
Mitchell JS, Glowacki J, Grandchamp AE, Manning RS, Maddocks JH "Sequence-Dependent Persistence Lengths of DNA." J Chem Theory Comput, 2017 https://doi.org/10.1021/acs.jctc.6b00904
PMID: 28029797
PMCID: None
Gonzalez O, Petkevičiūtė D, Maddocks JH "A sequence-dependent rigid-base model of DNA." J Chem Phys, 2013 https://doi.org/10.1063/1.4789411
PMID: 23406150
O. Gonzalez, M. Pasi, D. Petkevičiūtė, J. Glowacki, J.H. Maddocks "Absolute versus relative entropy parameter estimation in a coarse-grain model of DNA" Multiscale Modeling and Simulation 15, no. 3 (2017), p. 1073 - 1107 https://doi.org/10.1137/16M1086091
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