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DNA Readout Viewer (DRV): visualization of specificity determining patterns of protein-binding DNA segments

SUMMARY: The sequence specific recognition of DNA by regulatory proteins typically occurs by establishing hydrogen bonds and non-bonded contacts between chemical sub-structures of nucleotides and amino acids forming the compatible interacting surfaces. The recognition process is also influenced by t...

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Detalles Bibliográficos
Autores principales: Adam, Krisztian, Gyorgypal, Zoltan, Hegedus, Zoltan
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Oxford University Press 2020
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7141859/
https://www.ncbi.nlm.nih.gov/pubmed/31793988
http://dx.doi.org/10.1093/bioinformatics/btz906
Descripción
Sumario:SUMMARY: The sequence specific recognition of DNA by regulatory proteins typically occurs by establishing hydrogen bonds and non-bonded contacts between chemical sub-structures 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 visualization of functional groups and a diverse collection of DNA descriptors. By applying its intuitive representation concept for various DNA recognition related visualization tasks, DRV can contribute to unravelling the binding specificity factors of DNA-protein interactions. AVAILABILITY AND IMPLEMENTATION: DRV is freely available at https://drv.brc.hu. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.