Inhibitors of Protein-Protein Interaction Database




Tutorial for Query mode

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.

Tutorial for Visualize pockets

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

Tutorial for Contribution mode

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

Tutorial for Analyze druggability / interactibility

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

Tutorial for Visualize hotspots and ligands

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

Tutorial for study closely related pockets

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

How to use the TMAP

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