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A comprehensive resource for integrating and displaying protein post-translational modifications.

Lee TY, Hsu JB, Chang WC, Wang TY, Hsu PC, Huang HD - BMC Res Notes (2009)

Bottom Line: Moreover, this work compiles a benchmark to construct evaluation datasets for computational study to identifying PTM sites, such as phosphorylated sites, glycosylated sites, acetylated sites and methylated sites.The current release not only provides the sequence-based information, but also annotates the structure-based information for protein post-translational modification.The interface is also designed to facilitate the access to the resource.

View Article: PubMed Central - HTML - PubMed

Affiliation: Department of Biological Science and Technology, Institute of Bioinformatics and Systems Biology, National Chiao Tung University, Hsin-Chu 300, Taiwan. francis.bi93g@nctu.edu.tw

ABSTRACT

Background: Protein Post-Translational Modification (PTM) plays an essential role in cellular control mechanisms that adjust protein physical and chemical properties, folding, conformation, stability and activity, thus also altering protein function.

Findings: dbPTM (version 1.0), which was developed previously, aimed on a comprehensive collection of protein post-translational modifications. In this update version (dbPTM2.0), we developed a PTM database towards an expert system of protein post-translational modifications. The database comprehensively collects experimental and predictive protein PTM sites. In addition, dbPTM2.0 was extended to a knowledge base comprising the modified sites, solvent accessibility of substrate, protein secondary and tertiary structures, protein domains, protein intrinsic disorder region, and protein variations. Moreover, this work compiles a benchmark to construct evaluation datasets for computational study to identifying PTM sites, such as phosphorylated sites, glycosylated sites, acetylated sites and methylated sites.

Conclusion: The current release not only provides the sequence-based information, but also annotates the structure-based information for protein post-translational modification. The interface is also designed to facilitate the access to the resource. This effective database is now freely accessible at http://dbPTM.mbc.nctu.edu.tw/.

No MeSH data available.


The system architecture of the knowledge base for protein translational modification. It comprises the three major components: integration of external experimental PTM databases, learning and prediction of 20 types of PTM, and annotations of PTM knowledge (more details in the text).
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Figure 1: The system architecture of the knowledge base for protein translational modification. It comprises the three major components: integration of external experimental PTM databases, learning and prediction of 20 types of PTM, and annotations of PTM knowledge (more details in the text).

Mentions: As shown in Figure 1, the system architecture of dbPTM2.0 database comprises three major components: the integration of external PTM databases, the computational identification of PTMs, and the structural and functional annotations of PTMs. We integrated five PTM databases, including UniProtKB/Swiss-Prot (release 55.0) [1], Phospho.ELM (version 7.0) [15], O-GLYCBASE (version 6.0) [8], UbiProt (version 1.0) [9] and PHOSIDA (version 1.0) [6] for obtaining experimental protein modifications. The description and data statistics of these databases are briefly given in Table S1 (see Additional file 1 – Table S1). Additionally, Human Protein Reference Database (HPRD) [16], which compiles invaluable information relevant to functions and PTMs of human proteins in health and disease, was also integrated.


A comprehensive resource for integrating and displaying protein post-translational modifications.

Lee TY, Hsu JB, Chang WC, Wang TY, Hsu PC, Huang HD - BMC Res Notes (2009)

The system architecture of the knowledge base for protein translational modification. It comprises the three major components: integration of external experimental PTM databases, learning and prediction of 20 types of PTM, and annotations of PTM knowledge (more details in the text).
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2713254&req=5

Figure 1: The system architecture of the knowledge base for protein translational modification. It comprises the three major components: integration of external experimental PTM databases, learning and prediction of 20 types of PTM, and annotations of PTM knowledge (more details in the text).
Mentions: As shown in Figure 1, the system architecture of dbPTM2.0 database comprises three major components: the integration of external PTM databases, the computational identification of PTMs, and the structural and functional annotations of PTMs. We integrated five PTM databases, including UniProtKB/Swiss-Prot (release 55.0) [1], Phospho.ELM (version 7.0) [15], O-GLYCBASE (version 6.0) [8], UbiProt (version 1.0) [9] and PHOSIDA (version 1.0) [6] for obtaining experimental protein modifications. The description and data statistics of these databases are briefly given in Table S1 (see Additional file 1 – Table S1). Additionally, Human Protein Reference Database (HPRD) [16], which compiles invaluable information relevant to functions and PTMs of human proteins in health and disease, was also integrated.

Bottom Line: Moreover, this work compiles a benchmark to construct evaluation datasets for computational study to identifying PTM sites, such as phosphorylated sites, glycosylated sites, acetylated sites and methylated sites.The current release not only provides the sequence-based information, but also annotates the structure-based information for protein post-translational modification.The interface is also designed to facilitate the access to the resource.

View Article: PubMed Central - HTML - PubMed

Affiliation: Department of Biological Science and Technology, Institute of Bioinformatics and Systems Biology, National Chiao Tung University, Hsin-Chu 300, Taiwan. francis.bi93g@nctu.edu.tw

ABSTRACT

Background: Protein Post-Translational Modification (PTM) plays an essential role in cellular control mechanisms that adjust protein physical and chemical properties, folding, conformation, stability and activity, thus also altering protein function.

Findings: dbPTM (version 1.0), which was developed previously, aimed on a comprehensive collection of protein post-translational modifications. In this update version (dbPTM2.0), we developed a PTM database towards an expert system of protein post-translational modifications. The database comprehensively collects experimental and predictive protein PTM sites. In addition, dbPTM2.0 was extended to a knowledge base comprising the modified sites, solvent accessibility of substrate, protein secondary and tertiary structures, protein domains, protein intrinsic disorder region, and protein variations. Moreover, this work compiles a benchmark to construct evaluation datasets for computational study to identifying PTM sites, such as phosphorylated sites, glycosylated sites, acetylated sites and methylated sites.

Conclusion: The current release not only provides the sequence-based information, but also annotates the structure-based information for protein post-translational modification. The interface is also designed to facilitate the access to the resource. This effective database is now freely accessible at http://dbPTM.mbc.nctu.edu.tw/.

No MeSH data available.