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DNAproDB: an interactive tool for structural analysis of DNA–protein complexes

Many biological processes are mediated by complex interactions between DNA and proteins. Transcription factors, various polymerases, nucleases and histones recognize and bind DNA with different levels of binding specificity. To understand the physical mechanisms that allow proteins to recognize DNA...

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Detalles Bibliográficos
Autores principales: Sagendorf, Jared M., Berman, Helen M., Rohs, Remo
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Oxford University Press 2017
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5570235/
https://www.ncbi.nlm.nih.gov/pubmed/28431131
http://dx.doi.org/10.1093/nar/gkx272
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author Sagendorf, Jared M.
Berman, Helen M.
Rohs, Remo
author_facet Sagendorf, Jared M.
Berman, Helen M.
Rohs, Remo
author_sort Sagendorf, Jared M.
collection PubMed
description Many biological processes are mediated by complex interactions between DNA and proteins. Transcription factors, various polymerases, nucleases and histones recognize and bind DNA with different levels of binding specificity. To understand the physical mechanisms that allow proteins to recognize DNA and achieve their biological functions, it is important to analyze structures of DNA–protein complexes in detail. DNAproDB is a web-based interactive tool designed to help researchers study these complexes. DNAproDB provides an automated structure-processing pipeline that extracts structural features from DNA–protein complexes. The extracted features are organized in structured data files, which are easily parsed with any programming language or viewed in a browser. We processed a large number of DNA–protein complexes retrieved from the Protein Data Bank and created the DNAproDB database to store this data. Users can search the database by combining features of the DNA, protein or DNA–protein interactions at the interface. Additionally, users can upload their own structures for processing privately and securely. DNAproDB provides several interactive and customizable tools for creating visualizations of the DNA–protein interface at different levels of abstraction that can be exported as high quality figures. All functionality is documented and freely accessible at http://dnaprodb.usc.edu.
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spelling pubmed-55702352017-08-29 DNAproDB: an interactive tool for structural analysis of DNA–protein complexes Sagendorf, Jared M. Berman, Helen M. Rohs, Remo Nucleic Acids Res Web Server Issue Many biological processes are mediated by complex interactions between DNA and proteins. Transcription factors, various polymerases, nucleases and histones recognize and bind DNA with different levels of binding specificity. To understand the physical mechanisms that allow proteins to recognize DNA and achieve their biological functions, it is important to analyze structures of DNA–protein complexes in detail. DNAproDB is a web-based interactive tool designed to help researchers study these complexes. DNAproDB provides an automated structure-processing pipeline that extracts structural features from DNA–protein complexes. The extracted features are organized in structured data files, which are easily parsed with any programming language or viewed in a browser. We processed a large number of DNA–protein complexes retrieved from the Protein Data Bank and created the DNAproDB database to store this data. Users can search the database by combining features of the DNA, protein or DNA–protein interactions at the interface. Additionally, users can upload their own structures for processing privately and securely. DNAproDB provides several interactive and customizable tools for creating visualizations of the DNA–protein interface at different levels of abstraction that can be exported as high quality figures. All functionality is documented and freely accessible at http://dnaprodb.usc.edu. Oxford University Press 2017-07-03 2017-04-20 /pmc/articles/PMC5570235/ /pubmed/28431131 http://dx.doi.org/10.1093/nar/gkx272 Text en © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research. http://creativecommons.org/licenses/by-nc/4.0/ This is an Open Access article distributed under the terms of the Creative Commons Attribution 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 Web Server Issue
Sagendorf, Jared M.
Berman, Helen M.
Rohs, Remo
DNAproDB: an interactive tool for structural analysis of DNA–protein complexes
title DNAproDB: an interactive tool for structural analysis of DNA–protein complexes
title_full DNAproDB: an interactive tool for structural analysis of DNA–protein complexes
title_fullStr DNAproDB: an interactive tool for structural analysis of DNA–protein complexes
title_full_unstemmed DNAproDB: an interactive tool for structural analysis of DNA–protein complexes
title_short DNAproDB: an interactive tool for structural analysis of DNA–protein complexes
title_sort dnaprodb: an interactive tool for structural analysis of dna–protein complexes
topic Web Server Issue
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5570235/
https://www.ncbi.nlm.nih.gov/pubmed/28431131
http://dx.doi.org/10.1093/nar/gkx272
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