ProteinVolume

ProteinVolume computes the solvent-excluded geometric volume components of proteins, specifically van der Waals and intramolecular void volumes, to quantify structural contributions relevant to pressure-induced unfolding.

Key Features:

• Solvent-excluded volume decomposition: Computes solvent-excluded geometric volume components of protein structures.
• Van der Waals volume calculation: Calculates the van der Waals volume contribution of protein atoms.
• Intramolecular void volume calculation: Determines internal void volumes within protein structures.
• Molecular surface generation: Generates molecular surfaces for proteins to define boundaries between protein and solvent.
• Flood-fill algorithm for volume quantification: Employs a flood-fill algorithm to precisely compute geometric volumes from generated molecular surfaces.
• Molecular surface volume metric: Provides a molecular surface volume metric for comparing structural changes.

Scientific Applications:

• Quantification of pressure-induced unfolding: Measures geometric volume changes that contribute to pressure unfolding of proteins.
• Isolation of hydration and geometric contributions: Separates van der Waals and intramolecular void volume components from hydration effects to assess solvent exposure during unfolding.
• Protein design for pressure response: Supports prediction and design of proteins with specific responses to changes in hydrostatic pressure using molecular surface volume metrics.

Methodology:

Generates molecular surfaces and employs a flood-fill algorithm to compute solvent-excluded geometric volume components, including van der Waals and intramolecular void volumes.