A comprehensive resource for integrating and displaying protein post-translational modifications
Tzong-Yi Lee1, Justin Bo-Kai Hsu, Wen-Chi Chang
1Department of Biological Science and Technology, Institute of Bioinformatics and Systems Biology, National Chiao Tung University, Hsin-Chu 300, Taiwan. francis.bi93g@nctu.edu.tw
BMC Research Notes
|June 25, 2009
Summary
The updated dbPTM2.0 database now serves as an expert system for protein post-translational modifications (PTMs). It integrates experimental and predicted PTM sites with structural and functional data, aiding computational studies.
Area of Science:
- Biochemistry
- Bioinformatics
- Molecular Biology
Background:
- Protein Post-Translational Modification (PTM) is crucial for cellular regulation, affecting protein properties, structure, and function.
- Understanding PTMs is essential for deciphering complex cellular control mechanisms.
Purpose of the Study:
- To develop an enhanced expert system for protein post-translational modifications.
- To create a comprehensive knowledge base integrating various data types related to PTMs.
- To provide a benchmark for evaluating computational PTM site identification methods.
Main Methods:
- Development of the dbPTM2.0 database, an updated version of the PTM collection.
- Integration of experimental and predicted protein PTM sites.
- Expansion of the knowledge base to include structural, domain, and variation data.
Main Results:
- dbPTM2.0 comprehensively collects and annotates protein PTM sites, including sequence and structure-based information.
- The database serves as a knowledge base with data on modified sites, accessibility, structures, domains, and variations.
- A benchmark for evaluating computational PTM site identification methods has been compiled.
Conclusions:
- The current release of dbPTM2.0 offers both sequence- and structure-based information for protein PTMs.
- The user-friendly interface facilitates access to this valuable resource.
- dbPTM2.0 is freely accessible, supporting research in PTM analysis.
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