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. 2020 Aug 19;10:13985. doi: 10.1038/s41598-020-70867-5

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© The Author(s) 2020

Open AccessThis article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/.

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Analysis of protein-DNA interactions observed in the MD simulation of Dre/rox (a) Projection of hydrogen bond interactions spotted in the last frame of the Dre/rox MD trajectory. The base-specific interactions with the minor groove are labeled with an asterisk (*). Hashes (#) denote the interactions with the DNA major groove. Nucplot was used to generate the image. (b) Detailed view of interactions observed in the PDI_BJ area of the Dre/rox complex based on MD simulations. The specificity-determining residues are highlighted with a yellow box. Hydrogen bonds are shown in black dashed lines and van der Waals interactions in dotted spheres. Pymol was used to generate the image (version 2.1, https://pymol.org/).