APID interactomes: providing proteome-based interactomes with controlled quality for multiple species and derived...

Area of Science:

• Bioinformatics
• Molecular Biology
• Systems Biology

Background:

• Protein-protein interactions (PPIs) are fundamental to cellular processes.
• Accessing curated, experimentally validated PPI data across diverse organisms is challenging.
• Existing resources often lack comprehensive integration and quality filtering of PPI information.

Purpose of the Study:

• To present APID (Agile Protein Interactomes DataServer), a newly redesigned, unified resource for protein interactomes.
• To provide access to experimentally validated protein-protein physical interactions for over 400 organisms.
• To facilitate the analysis and visualization of protein-protein interaction networks.

Main Methods:

• Integration of experimentally validated protein-protein physical interactions from primary databases and repositories.
• Analysis of 8,388 experimentally resolved 3D structures to identify specific PPIs.
• Development of a graph tool (Cytoscape.js) for interactive network visualization and analysis.

Main Results:

• APID offers a comprehensive collection of protein interactomes for >400 organisms, with 25 species having >500 interactions.
• The server provides access to 90,379 distinct proteins and 678,441 singular interactions.
• Information on experimental validation is included for each PPI, enabling quality-based filtering.

Conclusions:

• APID serves as a valuable, freely accessible resource for researchers studying protein interactomes.
• The unified and validated nature of the data supports robust interactome analysis and discovery.
• The integrated visualization tool enhances the exploration of complex protein interaction networks.