CavitySpace

CavitySpace catalogs potential ligand binding sites across the human proteome to support protein function inference and structure-based drug discovery.

Key Features:

• Extensive Coverage: CavitySpace represents the first comprehensive pocket library encompassing all proteins within the human proteome and applies the ligand binding site detection program CAVITY to identify potential binding sites.
• Integration with AlphaFold Predictions: The database incorporates 3D structures predicted by AlphaFold to extend analysis to proteins lacking experimental structural data.
• Validation and Recovery: CavitySpace recovers known ligand binding sites, providing validation of predicted cavities.
• Functional Grouping: Predicted binding sites are grouped by similarity to facilitate protein function prediction and drug repurposing analyses.
• Novel Opportunities for Drug Discovery: The resource identifies novel binding sites within highly reliable predicted structure regions, offering new targets for drug discovery.

Scientific Applications:

• Protein Function Prediction: Analysis of binding site locations and properties supports inference of protein functions.
• Structure-Based Drug Design: Detailed information on potential binding sites aids design of molecules targeting those sites.
• Drug Repurposing Studies: Grouping of similar binding sites enables exploration of new applications for existing drugs.

Methodology:

CavitySpace detects ligand binding sites using the CAVITY program applied to 3D protein structures predicted by AlphaFold.