A short video that shows how to use the new web application to rapidly build tailored and complex queries to iPPI-DB and share data with colleagues.

This tutorial guides the user on how to:

• navigate and access the Protein Interaction Explorer (PIE) section of the IPPIDB web-server
• view list of PIE functionalities
• display all available pockets in PIE as an “Overview” list
• search for any protein they want to visualize
• open the PIE 3D viewer to display the protein chains and associated pockets
• move/zoom 3D structures on the viewer

A short video that shows how you can efficiently add new data to iPPI-DB using the contribute mode and your ORCID ID.

This tutorial shows how to use the PIE (Protein Interaction Explorer) 3D viewer to:

• display and scale druggability prediction scores by InDeep^* and superpose them on the 3D protein structures
• display and scale InDeep^*predicted interactibility scores superposed on 3D protein structures

^*Indeep: V. Mallet, L. Ruano, A. Franel, M. Nilges, K. Druart, G.Bouvier, O.Sperandio, InDeep: 3D fully convolutional neural networks to assist in silico drug design on protein-protein interactions, Bioinformatics, Volume 38, Issue 5, March 2022, Pages 1261-1268

This tutorial shows how to use the PIE (Protein Interaction Explorer) 3D viewer to:

• visualize hotspots detected by FoldX for a protein complex
• visualize ligands superposed with chains of related proteins
• show colocalization of ligands with predicted hot spots

This tutorial shows how one can:

• explore the “Pockets” section of the PIE
• for a given pocket on a displayed protein, display list of all similar pockets from the iPPI-DB database
• display PSI metric (Pocket Similarity Index) for all the pockets with respect to the given pocket
• display list of physio-chemical descriptors for all the “similar” pockets

This tutorial shows how to:

• access and use the TMAP (pocketome) feature of PIE (Protein Interaction Explorer)
• Use the “Chart Help” feature to learn how to navigate the TMAP
• meaning of different criteria or legends which can be viewed on TMAP
• color code TMAP with different criteria
• search and query information for a complex via TMAP window
• format the names of HD (heterodimer) and PL (protein-ligand) pockets