Fig. 1

Pipeline for the comparison of protein-protein and protein-ligand analyses. a General pipeline: the structures for PLIs are downloaded from PDB and those for PPIs from Interactome3D. We use the BioJava library to extract protein-protein and protein-ligand contacts. Finally, we calculate the intersection between PPI and PLI contacts to identify the drugs that may interfere with the PPIs. b Visualization and analyses with IGB/MI-Bundle: we select a gene of interest in IGB and run the plugin twice: 1) on Interactome3D, with the PPI option, 2) on PDB, with the Small Molecules option. For each query, a result table is generated. We select the PPI and PLI interaction of interest in the respective table and for each of them we press the “create track” button. The generated tracks show all the residues of the selected protein that are in contact in a given interaction. We select both tracks and calculate the intersection (right click, then “track operations” and “Intersection”). IGB creates a new track where all residues of the selected protein that are in contact with the other protein and the small molecule are shown