DNA Readout Viewer (DRV) : Visualisation of Specificity Determining Patterns of Protein-Binding DNA Segments

Ádám, Krisztián and Györgypál, Zoltán and Hegedűs, Zoltán (2019) DNA Readout Viewer (DRV) : Visualisation of Specificity Determining Patterns of Protein-Binding DNA Segments. BIOINFORMATICS, 36 (7). pp. 2286-2287. ISSN 1367-4803 (print); 1460-2059 (online)

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Abstract

The sequence specific recognition of DNA by regulatory proteins typically occurs by establishing hydrogen bonds and non-bonded contacts between chemical substructures of nucleotides and amino acids forming the compatible interacting surfaces. The recognition process is also influenced by the physicochemical and conformational character of the target oligonucleotide motif. Although the role of these mechanisms in DNA-protein interactions is well-established, bioinformatical methods rarely address them directly, instead binding specificity is mostly assessed at nucleotide level. DNA Readout Viewer (DRV) aims to provide a novel DNA representation, facilitating in-depth view into these mechanisms by the concurrent visualisation of functional groups and a diverse collection of DNA descriptors. By applying its intuitive representation concept for various DNA recognition related visualisation tasks, DRV can contribute to unravelling the binding specificity factors of DNA-protein interactions.DRV is freely available at https://drv.brc.hu.Supplementary data are available at Bioinformatics online.

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