PTMOracle is a Cytoscape app that allows users to integrate different types of protein data into PPI networks. This includes the protein sequence, PTM sites and annotations such as domains, motifs and disordered regions. When running PTMOracle, users have access to several analytical tools that perform PTM-related queries. With these queries, users can develop systematic searches within the Cytoscape environment. These can highlight proteins of interest and explore network visualisations that address complex PTM-associated relationships. PTM sites can also be mapped on to protein sequences and annotations to help generate hypotheses about PTMs and their roles in PPIs.
**If you use PTMOracle in your research, please cite:**
Aidan P Tay, Chi Nam Ignatius Pang, Daniel L Winter, and Marc R. Wilkins. PTMOracle: a Cytoscape app for co-visualising and co-analysing post-translational modifications in protein interaction networks. *J. Proteome Res.* **2017** 16 (5) 1988-2003.