Table 4.
Tools for protein interaction analyses that can also be useful in PTM context.
| Name | Description | Accessibility | Reference |
|---|---|---|---|
| STRING | A database of known and predicted protein–protein interactions from experimental and knowledgebase sources | https://string-db.org/ | [190] |
| NetworkKIN | An approach for motif-based predictions of kinases and phosphoproteins | http://networkin.info/ | [184] |
| Cytoscape | An open source software for molecular interaction networks integration, analysis and visualization, along with gene annotations | https://cytoscape.org/ | [191] |
| ProHits-viz | A suit of tools to perform analysis and visualization of quantitative protein interaction data | https://prohits-viz.lunenfeld.ca/ | [159] |
| PTMOracle | A Cytoscape application for co-visualization and co-analysis of PTMs and protein-protein interactions | http://apps.cytoscape.org/apps/ptmoracle | [192] |
| NetworkAnalyst | An integrated tool to perform gene annotations and protein-protein interaction network analysis along with visualizations | http://www.networkanalyst.ca/ | [193] |