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A Fast and Quantitative Method for Post-translational Modification and Variant Enabled Mapping of Peptides to Genomes
Published on: May 22, 2018
PTMcode: a database of known and predicted functional associations between post-translational modifications in
Pablo Minguez1, Ivica Letunic, Luca Parca
1European Molecular Biology Laboratory, Meyerhofstrasse 1, 69117 Heidelberg, Germany.
Nucleic Acids Research
|November 30, 2012
Summary
The PTMcode database compiles known and predicted post-translational modification (PTM) associations in eukaryotes. This resource aids in understanding the PTM code, which regulates protein function through combinatorial modification states.
Area of Science:
- Molecular Biology
- Proteomics
- Bioinformatics
Background:
- Post-translational modifications (PTMs) are crucial for eukaryotic protein regulation and structural stability.
- Combinations of PTMs, termed the PTM code, modulate cellular functions.
- High-throughput technologies are generating vast amounts of PTM site data, enabling comparative analyses.
Purpose of the Study:
- To develop PTMcode, a database compiling known and predicted PTM associations.
- To provide a framework for hypothesis-driven analysis of PTM codes at various scales.
- To facilitate the study of PTM interplay within eukaryotic proteomes.
Main Methods:
- PTMcode integrates data from literature surveys, residue co-evolution, structural proximity, and PTM hotspots.
- The database covers 13 PTM types across 8 eukaryotic species.
- It utilizes five distinct evidence channels to establish PTM functional associations.
Main Results:
- The first release of PTMcode offers functional associations for PTMs within eukaryotic proteins.
- It provides context for the co-regulation of approximately 75,000 residues in over 10,000 proteins.
- The database is searchable and features an interactive web interface.
Conclusions:
- PTMcode serves as a valuable resource for exploring the complexity of the PTM code.
- It enables computational and experimental investigations into PTM combinatorial regulation.
- The database supports a deeper understanding of how PTMs collectively influence protein function and cellular processes.
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