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Allows users to develop systematic searches for proteins of interest and explore network visualisations that address complex post-translational modifications of proteins (PTM)-associated relationships. PTMOracle is a Cytoscape app for co-analysing PTMs within protein-protein interaction (PPI) networks. It also allows extensive data to be integrated and co-analysed with PPI networks, allowing the role of domains, motifs and disordered regions to be considered. For proteins of interest, or a whole proteome, PTMOracle can generate network visualisations to reveal complex PTM-associated relationships.
PtmPPIR / Prediction of Post-translational Modification Sites in Protein-Protein Interacting Regions
Predicts whether sites of protein modifications are inside or outside of protein-protein interacting regions (PPIRs), based on the existing structural and post-translational modifications (PTM) databases. PtmPPIR showed high performance measures, and important features contributing to predictive power were identified. The models were evaluated using 10 independent iterations of 5-fold cross-validation, and the resulting calculated performance measures for the models were high.
Enables identification of peptide modifications. Comet-PTM is an engine that takes account of the mass shift produced by the modification in the fragmentation series, producing the same score as a conventional “closed” searches (CS) using the same mass increment as a variable modification. It resolves the modification mass shift in the fragmentation series, doubling the number of modified peptides identified by conventional OS and matching the identification performance of targeted CS.
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