ProPores2

ProPores2 identifies and analyzes pores, surface pockets, cavities, and tunnels in protein structures to characterize structural features relevant to enzymatic catalysis, ligand binding, and ion/molecule transport.

Key Features:

• Pore Identification: Detects pores, surface pockets, cavities, and tunnels within protein structures.
• Axis Determination: Computes pore axes to characterize pore geometry and orientation.
• Opening Closed Connections: Performs side-chain rotations to open closed connections and reveal potential pathways in static protein models.
• Parallel Batch Processing: Processes multiple protein structures simultaneously using parallel batch analysis.
• Implementation: Implemented in C++.

Scientific Applications:

• Structural analysis: Characterizes pore spatial configurations and their functional implications in protein structures.
• Enzymatic catalysis: Supports investigation of channels and cavities involved in enzymatic activity.
• Ligand interaction studies: Aids analysis of ligand access and binding through pores and tunnels.
• Molecular transport: Facilitates study of ion and small-molecule transport across biomembranes via pores and tunnels.

Methodology:

Applies algorithms for pore identification and axis computation, performs side-chain rotations to open closed connections, and supports parallel batch processing for simultaneous analysis of multiple structures.