CAVER Web

CAVER Web integrates Caver 3.02-based tunnel identification with CaverDock 1.0 ligand transport analysis to identify protein tunnels and characterize ligand passage energetics and trajectories.

Key Features:

• Tunnel detection (Caver 3.02): Identifies tunnels and channels in protein structures using the Caver 3.02 algorithm.
• Ligand transport simulation (CaverDock 1.0): Simulates ligand passage through identified tunnels and computes associated energetics using CaverDock 1.0.
• Input types: Accepts protein structures and user-provided lists of ligands for transport analysis.
• Tunnel and ligand properties: Calculates tunnel geometry and physicochemical properties relevant to transport.
• Energy profiles: Computes energy profiles along ligand passage pathways.
• Ligand trajectories: Produces ligand passage trajectories through detected tunnels.
• Visualization outputs: Generates visual representations of tunnels, energy profiles, and ligand trajectories.
• Throughput and runtime: Typical processing times range from approximately 2 to 20 minutes per job, supporting virtual screening workflows.

Scientific Applications:

• Drug discovery: Characterizing ligand passage and energetics to inform inhibitor or ligand design and optimization.
• Protein engineering: Guiding mutations or modifications to alter tunnel geometry and transport properties.
• Virtual screening: Enabling high-throughput assessment of ligand transport through protein tunnels.
• Molecular transport studies: Investigating mechanisms of ligand transit and tunnel-mediated diffusion in proteins.

Methodology:

Caver 3.02 performs tunnel detection on input protein structures, and CaverDock 1.0 simulates ligand transport for provided ligand lists to compute energy profiles and ligand passage trajectories.