CaviDB

CaviDB catalogs cavities in protein structures and characterizes their structural, conformational, and chemical features to support analysis of ligand binding, enzyme catalysis, and drug-target identification.

Key Features:

• Integration with Detection Software: Integrates outputs from widely-used cavity detection software to identify protein cavities.
• Comprehensive Data Collection: Contains approximately 927,773 distinct proteins and characterizes over 36 million cavities, with more than 1.1 million predicted as potential drug targets.
• Linkage with Protein Conformers: Links each cavity entry to corresponding protein conformers to enable analysis of conformational changes.
• Functional and Structural Analysis Integration: Combines sequence, structural, and functional analyses to annotate cavity features relevant to mechanism.
• Drug Design and Discovery Applications: Enables comparison of cavities across conformational states to aid identification and prioritization of potential therapeutic targets.
• Research Utility: Supports investigations of protein structure–function relationships, pharmacology, and molecular biology.

Scientific Applications:

• Protein–Ligand Interaction Analysis: Provides cavity size, dynamics, and chemical property data to analyze binding sites and interactions.
• Enzyme Catalysis Studies: Enables examination of cavity microenvironments relevant to catalytic mechanisms.
• Target Identification for Drug Discovery: Supplies a large dataset of predicted druggable cavities for prioritizing therapeutic candidates.
• Comparative Conformational Studies: Supports comparison of cavities across conformers to study structural dynamics and functional implications.

Methodology:

Integrates outputs from cavity detection software with sequence-, structure-, and function-derived feature analyses and links cavities to corresponding protein conformers for comparative conformational studies.