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| Item Type: | Article |
|---|---|
| Title: | PTMcode: a database of known and predicted functional associations between post-translational modifications in proteins |
| Creators Name: | Minguez, P., Letunic, I., Parca, L. and Bork, P. |
| Abstract: | 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. |
| Keywords: | Internet, Molecular Evolution, Protein Databases, Proteins, Translational Protein Modification, Tertiary Protein Structure, User-Computer Interface, Animals, Cattle, Mice, Rats |
| Source: | Nucleic Acids Research |
| ISSN: | 0305-1048 |
| Publisher: | Oxford University Press |
| Volume: | 41 |
| Number: | D1 |
| Page Range: | D306-D311 |
| Date: | 1 January 2013 |
| Official Publication: | https://doi.org/10.1093/nar/gks1230 |
| PubMed: | View item in PubMed |
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