Volarea

Volarea computes solvent-exposed surface areas, inter-molecular contact areas, molecular volumes, and cavity volumes from molecular structures to quantitatively characterize interfaces, tunnels, clefts, and spatial occupancy.

Key Features:

• Solvent-exposed surface area: Computes the solvent-exposed surface area of molecules for analysis of solvent interactions.
• Inter-molecular contact area: Determines the contact area between two interacting molecules to characterize interfaces.
• Molecular volume: Calculates the volume occupied by molecular structures to assess spatial occupancy.
• Cavity and tunnel volume: Assesses volumes of molecular cavities, including tunnels and clefts, relevant to pathways and binding sites.
• Automated analysis: Performs rapid, fully automated calculations of surface and volume metrics.
• VMD integration: Implemented as a plug-in for Visual Molecular Dynamics (VMD) to operate within the VMD environment.

Scientific Applications:

• Protein/Ligand Complexes: Quantifies binding-interface and solvent-exposed areas to support analysis of interactions and affinity.
• Enzyme Active Sites: Analyzes spatial configurations of active sites relevant to catalytic activity.
• Protein/Protein Interfaces: Studies interaction surfaces that mediate complex formation and cellular functions.
• Enzyme Channels and Membrane Pores: Investigates pathways through which molecules traverse biological membranes.
• Solvent Tunnels: Explores internal channels within proteins that facilitate solvent movement.

Methodology:

Employs advanced algorithms to automate calculation of surface areas, contact areas, molecular volumes and cavity volumes; provided as a plug-in for Visual Molecular Dynamics (VMD) to perform analyses within the VMD environment.