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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...
Autores principales: | , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Oxford University Press
2020
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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 |
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author | Adam, Krisztian Gyorgypal, Zoltan Hegedus, Zoltan |
author_facet | Adam, Krisztian Gyorgypal, Zoltan Hegedus, Zoltan |
author_sort | Adam, Krisztian |
collection | PubMed |
description | 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. |
format | Online Article Text |
id | pubmed-7141859 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2020 |
publisher | Oxford University Press |
record_format | MEDLINE/PubMed |
spelling | pubmed-71418592020-04-13 DNA Readout Viewer (DRV): visualization of specificity determining patterns of protein-binding DNA segments Adam, Krisztian Gyorgypal, Zoltan Hegedus, Zoltan Bioinformatics Applications Notes 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. Oxford University Press 2020-04-01 2019-12-03 /pmc/articles/PMC7141859/ /pubmed/31793988 http://dx.doi.org/10.1093/bioinformatics/btz906 Text en © The Author(s) 2019. Published by Oxford University Press. http://creativecommons.org/licenses/by-nc/4.0/ This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/4.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact journals.permissions@oup.com |
spellingShingle | Applications Notes Adam, Krisztian Gyorgypal, Zoltan Hegedus, Zoltan DNA Readout Viewer (DRV): visualization of specificity determining patterns of protein-binding DNA segments |
title | DNA Readout Viewer (DRV): visualization of specificity determining patterns of protein-binding DNA segments |
title_full | DNA Readout Viewer (DRV): visualization of specificity determining patterns of protein-binding DNA segments |
title_fullStr | DNA Readout Viewer (DRV): visualization of specificity determining patterns of protein-binding DNA segments |
title_full_unstemmed | DNA Readout Viewer (DRV): visualization of specificity determining patterns of protein-binding DNA segments |
title_short | DNA Readout Viewer (DRV): visualization of specificity determining patterns of protein-binding DNA segments |
title_sort | dna readout viewer (drv): visualization of specificity determining patterns of protein-binding dna segments |
topic | Applications Notes |
url | 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 |
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