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PTMcode: a database of known and predicted functional associations between post-translational modifications in proteins
Post-translational modifications (PTMs) are involved in the regulation and structural stabilization of eukaryotic proteins. The combination of individual PTM states is a key to modulate cellular functions as became evident in a few well-studied proteins. This combinatorial setting, dubbed the PTM co...
Autores principales: | , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Oxford University Press
2013
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3531129/ https://www.ncbi.nlm.nih.gov/pubmed/23193284 http://dx.doi.org/10.1093/nar/gks1230 |
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author | Minguez, Pablo Letunic, Ivica Parca, Luca Bork, Peer |
author_facet | Minguez, Pablo Letunic, Ivica Parca, Luca Bork, Peer |
author_sort | Minguez, Pablo |
collection | PubMed |
description | Post-translational modifications (PTMs) are involved in the regulation and structural stabilization of eukaryotic proteins. The combination of individual PTM states is a key to modulate cellular functions as became evident in a few well-studied proteins. This combinatorial setting, dubbed the PTM code, has been proposed to be extended to whole proteomes in eukaryotes. Although we are still far from deciphering such a complex language, thousands of protein PTM sites are being mapped by high-throughput technologies, thus providing sufficient data for comparative analysis. PTMcode (http://ptmcode.embl.de) aims to compile known and predicted PTM associations to provide a framework that would enable hypothesis-driven experimental or computational analysis of various scales. In its first release, PTMcode provides PTM functional associations of 13 different PTM types within proteins in 8 eukaryotes. They are based on five evidence channels: a literature survey, residue co-evolution, structural proximity, PTMs at the same residue and location within PTM highly enriched protein regions (hotspots). PTMcode is presented as a protein-based searchable database with an interactive web interface providing the context of the co-regulation of nearly 75 000 residues in >10 000 proteins. |
format | Online Article Text |
id | pubmed-3531129 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2013 |
publisher | Oxford University Press |
record_format | MEDLINE/PubMed |
spelling | pubmed-35311292013-03-07 PTMcode: a database of known and predicted functional associations between post-translational modifications in proteins Minguez, Pablo Letunic, Ivica Parca, Luca Bork, Peer Nucleic Acids Res Articles Post-translational modifications (PTMs) are involved in the regulation and structural stabilization of eukaryotic proteins. The combination of individual PTM states is a key to modulate cellular functions as became evident in a few well-studied proteins. This combinatorial setting, dubbed the PTM code, has been proposed to be extended to whole proteomes in eukaryotes. Although we are still far from deciphering such a complex language, thousands of protein PTM sites are being mapped by high-throughput technologies, thus providing sufficient data for comparative analysis. PTMcode (http://ptmcode.embl.de) aims to compile known and predicted PTM associations to provide a framework that would enable hypothesis-driven experimental or computational analysis of various scales. In its first release, PTMcode provides PTM functional associations of 13 different PTM types within proteins in 8 eukaryotes. They are based on five evidence channels: a literature survey, residue co-evolution, structural proximity, PTMs at the same residue and location within PTM highly enriched protein regions (hotspots). PTMcode is presented as a protein-based searchable database with an interactive web interface providing the context of the co-regulation of nearly 75 000 residues in >10 000 proteins. Oxford University Press 2013-01 2012-11-27 /pmc/articles/PMC3531129/ /pubmed/23193284 http://dx.doi.org/10.1093/nar/gks1230 Text en © The Author(s) 2012. Published by Oxford University Press. http://creativecommons.org/licenses/by-nc/3.0 This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by-nc/3.0/), which permits non-commercial reuse, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact journals.permissions@oup.com. |
spellingShingle | Articles Minguez, Pablo Letunic, Ivica Parca, Luca Bork, Peer PTMcode: a database of known and predicted functional associations between post-translational modifications in proteins |
title | PTMcode: a database of known and predicted functional associations between post-translational modifications in proteins |
title_full | PTMcode: a database of known and predicted functional associations between post-translational modifications in proteins |
title_fullStr | PTMcode: a database of known and predicted functional associations between post-translational modifications in proteins |
title_full_unstemmed | PTMcode: a database of known and predicted functional associations between post-translational modifications in proteins |
title_short | PTMcode: a database of known and predicted functional associations between post-translational modifications in proteins |
title_sort | ptmcode: a database of known and predicted functional associations between post-translational modifications in proteins |
topic | Articles |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3531129/ https://www.ncbi.nlm.nih.gov/pubmed/23193284 http://dx.doi.org/10.1093/nar/gks1230 |
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