Related Experiment Video
Updated: Jun 28, 2025

Author Spotlight: Streamlining Protein Target Prediction and Validation via Molecular Docking and CETSA
Published on: February 23, 2024
A comprehensive dataset of protein-protein interactions and ligand binding pockets for advancing drug discovery
Alexandra Moine-Franel1,2, Fabien Mareuil1, Michael Nilges1
1Structural Bioinformatics Unit, Department of Structural Biology and Chemistry, Institut Pasteur, Université de Paris, CNRS UMR3528, Paris, France.
Abstract:
This dataset represents a collection of pocket-centric structural data related to protein-protein interactions (PPIs) and PPI-related ligand binding sites. The dataset includes high-quality structural information on more than 23,000 pockets, 3,700 proteins on more than 500 organisms, and nearly 3500 ligands that can aid researchers in the fields of bioinformatics, structural biology, and drug discovery. It encompasses a diverse set of PPI complexes with more than 1,700 unique protein families including some with associated ligands, enabling detailed investigations into molecular interactions at the atomic level. This article introduces an indispensable resource designed to unlock the full potential of PPIs while pioneering a novel metric for pocket similarity for hypothesizing protein partners repurposing.
More Related Videos
08:31Biosensor-based High Throughput Biopanning and Bioinformatics Analysis Strategy for the Global Validation of Drug-protein Interactions
Published on: December 1, 2020
11:19Label-Free Immunoprecipitation Mass Spectrometry Workflow for Large-scale Nuclear Interactome Profiling
Published on: November 17, 2019
Related Concept Videos
Protein-protein Interfaces
Ligand Binding Sites
Protein-ligand interactions are quite specific; even though numerous potential ligands surround a cellular protein at any given time, only a particular ligand can bind to that protein. Moreover, a ligand binds only to a dedicated area on the surface of the protein, known as the...
Protein Networks
These interactions can be represented through maps depicting protein-protein interaction networks, represented as nodes and edges. Nodes are circles that are representative of a protein,...
Conserved Binding Sites
Binding sites are often located in large pockets, and if their location on a protein’s surface is unknown, it can be predicted using various approaches. The energetic method computationally...
The Equilibrium Binding Constant and Binding Strength
Protein-Drug Binding: Determination Methods
Indirect methods involve isolating the bound drug from its free form in biological samples such as blood, serum, or plasma. These techniques aim to measure the percentage of drugs bound to proteins. Equilibrium dialysis is a commonly used method where the free drug concentration at equilibrium is measured by separating the bound...