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dbPTM 3.0: an informative resource for investigating substrate site specificity and functional association of protein post-translational modifications

Protein modification is an extremely important post-translational regulation that adjusts the physical and chemical properties, conformation, stability and activity of a protein; thus altering protein function. Due to the high throughput of mass spectrometry (MS)-based methods in identifying site-sp...

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Autores principales: Lu, Cheng-Tsung, Huang, Kai-Yao, Su, Min-Gang, Lee, Tzong-Yi, Bretaña, Neil Arvin, Chang, Wen-Chi, Chen, Yi-Ju, Chen, Yu-Ju, Huang, Hsien-Da
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Oxford University Press 2013
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3531199/
https://www.ncbi.nlm.nih.gov/pubmed/23193290
http://dx.doi.org/10.1093/nar/gks1229
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author Lu, Cheng-Tsung
Huang, Kai-Yao
Su, Min-Gang
Lee, Tzong-Yi
Bretaña, Neil Arvin
Chang, Wen-Chi
Chen, Yi-Ju
Chen, Yu-Ju
Huang, Hsien-Da
author_facet Lu, Cheng-Tsung
Huang, Kai-Yao
Su, Min-Gang
Lee, Tzong-Yi
Bretaña, Neil Arvin
Chang, Wen-Chi
Chen, Yi-Ju
Chen, Yu-Ju
Huang, Hsien-Da
author_sort Lu, Cheng-Tsung
collection PubMed
description Protein modification is an extremely important post-translational regulation that adjusts the physical and chemical properties, conformation, stability and activity of a protein; thus altering protein function. Due to the high throughput of mass spectrometry (MS)-based methods in identifying site-specific post-translational modifications (PTMs), dbPTM (http://dbPTM.mbc.nctu.edu.tw/) is updated to integrate experimental PTMs obtained from public resources as well as manually curated MS/MS peptides associated with PTMs from research articles. Version 3.0 of dbPTM aims to be an informative resource for investigating the substrate specificity of PTM sites and functional association of PTMs between substrates and their interacting proteins. In order to investigate the substrate specificity for modification sites, a newly developed statistical method has been applied to identify the significant substrate motifs for each type of PTMs containing sufficient experimental data. According to the data statistics in dbPTM, >60% of PTM sites are located in the functional domains of proteins. It is known that most PTMs can create binding sites for specific protein-interaction domains that work together for cellular function. Thus, this update integrates protein–protein interaction and domain–domain interaction to determine the functional association of PTM sites located in protein-interacting domains. Additionally, the information of structural topologies on transmembrane (TM) proteins is integrated in dbPTM in order to delineate the structural correlation between the reported PTM sites and TM topologies. To facilitate the investigation of PTMs on TM proteins, the PTM substrate sites and the structural topology are graphically represented. Also, literature information related to PTMs, orthologous conservations and substrate motifs of PTMs are also provided in the resource. Finally, this version features an improved web interface to facilitate convenient access to the resource.
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spelling pubmed-35311992013-03-07 dbPTM 3.0: an informative resource for investigating substrate site specificity and functional association of protein post-translational modifications Lu, Cheng-Tsung Huang, Kai-Yao Su, Min-Gang Lee, Tzong-Yi Bretaña, Neil Arvin Chang, Wen-Chi Chen, Yi-Ju Chen, Yu-Ju Huang, Hsien-Da Nucleic Acids Res Articles Protein modification is an extremely important post-translational regulation that adjusts the physical and chemical properties, conformation, stability and activity of a protein; thus altering protein function. Due to the high throughput of mass spectrometry (MS)-based methods in identifying site-specific post-translational modifications (PTMs), dbPTM (http://dbPTM.mbc.nctu.edu.tw/) is updated to integrate experimental PTMs obtained from public resources as well as manually curated MS/MS peptides associated with PTMs from research articles. Version 3.0 of dbPTM aims to be an informative resource for investigating the substrate specificity of PTM sites and functional association of PTMs between substrates and their interacting proteins. In order to investigate the substrate specificity for modification sites, a newly developed statistical method has been applied to identify the significant substrate motifs for each type of PTMs containing sufficient experimental data. According to the data statistics in dbPTM, >60% of PTM sites are located in the functional domains of proteins. It is known that most PTMs can create binding sites for specific protein-interaction domains that work together for cellular function. Thus, this update integrates protein–protein interaction and domain–domain interaction to determine the functional association of PTM sites located in protein-interacting domains. Additionally, the information of structural topologies on transmembrane (TM) proteins is integrated in dbPTM in order to delineate the structural correlation between the reported PTM sites and TM topologies. To facilitate the investigation of PTMs on TM proteins, the PTM substrate sites and the structural topology are graphically represented. Also, literature information related to PTMs, orthologous conservations and substrate motifs of PTMs are also provided in the resource. Finally, this version features an improved web interface to facilitate convenient access to the resource. Oxford University Press 2013-01 2012-11-26 /pmc/articles/PMC3531199/ /pubmed/23193290 http://dx.doi.org/10.1093/nar/gks1229 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
Lu, Cheng-Tsung
Huang, Kai-Yao
Su, Min-Gang
Lee, Tzong-Yi
Bretaña, Neil Arvin
Chang, Wen-Chi
Chen, Yi-Ju
Chen, Yu-Ju
Huang, Hsien-Da
dbPTM 3.0: an informative resource for investigating substrate site specificity and functional association of protein post-translational modifications
title dbPTM 3.0: an informative resource for investigating substrate site specificity and functional association of protein post-translational modifications
title_full dbPTM 3.0: an informative resource for investigating substrate site specificity and functional association of protein post-translational modifications
title_fullStr dbPTM 3.0: an informative resource for investigating substrate site specificity and functional association of protein post-translational modifications
title_full_unstemmed dbPTM 3.0: an informative resource for investigating substrate site specificity and functional association of protein post-translational modifications
title_short dbPTM 3.0: an informative resource for investigating substrate site specificity and functional association of protein post-translational modifications
title_sort dbptm 3.0: an informative resource for investigating substrate site specificity and functional association of protein post-translational modifications
topic Articles
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3531199/
https://www.ncbi.nlm.nih.gov/pubmed/23193290
http://dx.doi.org/10.1093/nar/gks1229
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