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Updated: May 16, 2026
06:50
Computational Prediction of Amino Acid Preferences of Potentially Multispecific Peptide-Binding Domains Involved in Protein-Protein Interactions
Published on: January 26, 2024
2P2Idb: a structural database dedicated to orthosteric modulation of protein-protein interactions
Marie Jeanne Basse1, Stéphane Betzi, Raphaël Bourgeas
1Laboratory of Integrative Structural and Chemical Biology (iSCB), Centre de Recherche en Cancérologie de Marseille (CRCM), CNRS UMR 7258, INSERM U 1068, Institut Paoli-Calmettes, Marseille, France.
Nucleic Acids Research
|December 4, 2012
Summary
A new database, 2P2Idb, catalogs protein-protein interactions with known modulators. It aids in understanding druggability by analyzing structural and biophysical properties of these interfaces.
Area of Science:
- Structural Biology
- Medicinal Chemistry
- Computational Biology
Background:
- Protein-protein interactions (PPIs) are crucial targets for next-generation therapeutics.
- Developing tools to target the complex chemical space of PPIs is essential.
- Recent successes highlight the need for systematic analysis of PPIs.
Purpose of the Study:
- To create a comprehensive, hand-curated structural database of PPIs with known orthosteric modulators.
- To identify common principles and druggability assessment criteria for PPIs.
- To provide a resource for researchers in academia and the pharmaceutical industry.
Main Methods:
- Construction of the 2P2Idb database, including PPIs with characterized protein-protein and protein-ligand complexes.
- Development of a web server with links to related sites, binding affinity data, and 3D interactive views.
- Analysis of PPI interfaces by comparing 2P2Idb data with representative heterodimeric complex datasets.
Main Results:
- The 2P2Idb database is freely accessible and contains hand-curated structural information.
- Identification of key geometrical parameters and residue properties for assessing PPI druggability.
- A tool was developed to compute various biophysical and geometrical descriptors of PPI interfaces.
Conclusions:
- The 2P2Idb database serves as a valuable structural information resource for targeting PPIs.
- The identified parameters and properties can guide the development of novel therapeutics for PPIs.
- The database and associated tools facilitate research in drug discovery for protein-protein interactions.
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