3V

3V identifies and analyzes internal volumes such as cavities, channels, and clefts in RNA and protein structures using solvent-excluded surface calculations.

Key Features:

• Automated Internal Volume Detection: Detects internal cavities, channels, and clefts within macromolecular structures using computational surface analysis.
• Solvent-Excluded Surface Comparison: Computes solvent-excluded surfaces with different probe radii to identify enclosed internal volumes.
• Volumetric Structural Representation: Generates volumetric representations of detected internal spaces for structural analysis.
• Image and Data Outputs: Produces visual images and downloadable files describing internal volumes for downstream structural analysis.

Scientific Applications:

• Macromolecular Function Analysis: Investigates structural cavities and channels associated with substrate binding, ion transport, and enzymatic activity.
• Structure-Based Drug Design: Identifies internal binding pockets and cavities that may serve as potential ligand or inhibitor binding sites.
• Structural Biology Studies: Analyzes internal structural features of RNA and protein macromolecules that influence biological function.

Methodology:

3V calculates solvent-excluded surfaces using two probe radii, including a standard solvent radius of approximately 1.5 Å and a maximized probe radius, and determines internal volumes by computing the difference between the resulting surfaces.