The Online Protein Processing Resource (TOPPR): a database and analysis platform for protein processing events
| Autor: | Kim Plasman, Davy Maddelein, Kris Gevaert, Lennart Martens, Petra Van Damme, Kenny Helsens, Niels Hulstaert, Niklaas Colaert, Joël Vandekerckhove, Francis Impens |
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| Jazyk: | angličtina |
| Rok vydání: | 2012 |
| Předmět: |
Biology
Proteomics computer.software_genre Conserved sequence Substrate Specificity 03 medical and health sciences Search engine Mice SUBSTRATE REVEALS Genetics Animals Humans Databases Protein Protein secondary structure 030304 developmental biology 0303 health sciences Internet IDENTIFICATION Database 030302 biochemistry & molecular biology Online database Proteolytic enzymes Biology and Life Sciences Proteins Articles Visualization PROTEASES CELL-DEATH Proteolysis LIBRARY PROTEOMICS GRANZYME UniProt computer Protein Processing Post-Translational Peptide Hydrolases |
| Zdroj: | Nucleic Acids Research Nucleic Acids Research; Vol 41 NUCLEIC ACIDS RESEARCH |
| ISSN: | 1362-4962 0305-1048 |
| Popis: | We here present The Online Protein Processing Resource (TOPPR; http://iomics.ugent.be/toppr/), an online database that contains thousands of published proteolytically processed sites in human and mouse proteins. These cleavage events were identified with COmbinded FRActional DIagonal Chromatography proteomics technologies, and the resulting database is provided with full data provenance. Indeed, TOPPR provides an interactive visual display of the actual fragmentation mass spectrum that led to each identification of a reported processed site, complete with fragment ion annotations and search engine scores. Apart from warehousing and disseminating these data in an intuitive manner, TOPPR also provides an online analysis platform, including methods to analyze protease specificity and substrate-centric analyses. Concretely, TOPPR supports three ways to retrieve data: (i) the retrieval of all substrates for one or more cellular stimuli or assays; (ii) a substrate search by UniProtKB/Swiss-Prot accession number, entry name or description; and (iii) a motif search that retrieves substrates matching a user-defined protease specificity profile. The analysis of the substrates is supported through the presence of a variety of annotations, including predicted secondary structure, known domains and experimentally obtained 3D structure where available. Across substrates, substrate orthologs and conserved sequence stretches can also be shown, with iceLogo visualization provided for the latter. |
| Databáze: | OpenAIRE |
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