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DBBP: database of binding pairs in protein-nucleic acid interactions

BACKGROUND: Interaction of proteins with other molecules plays an important role in many biological activities. As many structures of protein-DNA complexes and protein-RNA complexes have been determined in the past years, several databases have been constructed to provide structure data of the compl...

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Autores principales: Park, Byungkyu, Kim, Hyungchan, Han, Kyungsook
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2014
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4271565/
https://www.ncbi.nlm.nih.gov/pubmed/25474259
http://dx.doi.org/10.1186/1471-2105-15-S15-S5
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author Park, Byungkyu
Kim, Hyungchan
Han, Kyungsook
author_facet Park, Byungkyu
Kim, Hyungchan
Han, Kyungsook
author_sort Park, Byungkyu
collection PubMed
description BACKGROUND: Interaction of proteins with other molecules plays an important role in many biological activities. As many structures of protein-DNA complexes and protein-RNA complexes have been determined in the past years, several databases have been constructed to provide structure data of the complexes. However, the information on the binding sites between proteins and nucleic acids is not readily available from the structure data since the data consists mostly of the three-dimensional coordinates of the atoms in the complexes. RESULTS: We analyzed the huge amount of structure data for the hydrogen bonding interactions between proteins and nucleic acids and developed a database called DBBP (DataBase of Binding Pairs in protein-nucleic acid interactions, http://bclab.inha.ac.kr/dbbp). DBBP contains 44,955 hydrogen bonds (H-bonds) of protein-DNA interactions and 77,947 H-bonds of protein-RNA interactions. CONCLUSIONS: Analysis of the huge amount of structure data of protein-nucleic acid complexes is labor-intensive, yet provides useful information for studying protein-nucleic acid interactions. DBBP provides the detailed information of hydrogen-bonding interactions between proteins and nucleic acids at various levels from the atomic level to the residue level. The binding information can be used as a valuable resource for developing a computational method aiming at predicting new binding sites in proteins or nucleic acids.
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spelling pubmed-42715652015-01-02 DBBP: database of binding pairs in protein-nucleic acid interactions Park, Byungkyu Kim, Hyungchan Han, Kyungsook BMC Bioinformatics Proceedings BACKGROUND: Interaction of proteins with other molecules plays an important role in many biological activities. As many structures of protein-DNA complexes and protein-RNA complexes have been determined in the past years, several databases have been constructed to provide structure data of the complexes. However, the information on the binding sites between proteins and nucleic acids is not readily available from the structure data since the data consists mostly of the three-dimensional coordinates of the atoms in the complexes. RESULTS: We analyzed the huge amount of structure data for the hydrogen bonding interactions between proteins and nucleic acids and developed a database called DBBP (DataBase of Binding Pairs in protein-nucleic acid interactions, http://bclab.inha.ac.kr/dbbp). DBBP contains 44,955 hydrogen bonds (H-bonds) of protein-DNA interactions and 77,947 H-bonds of protein-RNA interactions. CONCLUSIONS: Analysis of the huge amount of structure data of protein-nucleic acid complexes is labor-intensive, yet provides useful information for studying protein-nucleic acid interactions. DBBP provides the detailed information of hydrogen-bonding interactions between proteins and nucleic acids at various levels from the atomic level to the residue level. The binding information can be used as a valuable resource for developing a computational method aiming at predicting new binding sites in proteins or nucleic acids. BioMed Central 2014-12-03 /pmc/articles/PMC4271565/ /pubmed/25474259 http://dx.doi.org/10.1186/1471-2105-15-S15-S5 Text en Copyright © 2014 Park et al.; licensee BioMed Central Ltd. http://creativecommons.org/licenses/by/4.0 This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.
spellingShingle Proceedings
Park, Byungkyu
Kim, Hyungchan
Han, Kyungsook
DBBP: database of binding pairs in protein-nucleic acid interactions
title DBBP: database of binding pairs in protein-nucleic acid interactions
title_full DBBP: database of binding pairs in protein-nucleic acid interactions
title_fullStr DBBP: database of binding pairs in protein-nucleic acid interactions
title_full_unstemmed DBBP: database of binding pairs in protein-nucleic acid interactions
title_short DBBP: database of binding pairs in protein-nucleic acid interactions
title_sort dbbp: database of binding pairs in protein-nucleic acid interactions
topic Proceedings
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4271565/
https://www.ncbi.nlm.nih.gov/pubmed/25474259
http://dx.doi.org/10.1186/1471-2105-15-S15-S5
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