CAVER PyMOL plugin

CAVER PyMOL plugin identifies and analyzes tunnels and channels in protein structures to characterize transport pathways that mediate small-molecule, ion, and solvent movement.

Key Features:

• Identification and characterization: Detects and characterizes tunnels and channels in protein structures, reporting geometric and physico-chemical properties.
• Advanced algorithms (CAVER 3.0): Implements the algorithms introduced in CAVER 3.0 to perform pathway calculations and clustering across large ensembles of conformations.
• Pathway clustering and ensemble analysis: Applies clustering algorithms to manage and interpret large datasets of protein conformations and to summarize pathway families.
• Transient tunnel detection: Identifies and estimates the importance of tunnels that appear in molecular dynamics ensembles but may be absent in static crystal structures.
• Molecular dynamics support: Accepts molecular dynamics simulation trajectories as input and analyzes time-resolved pathway evolution.

Scientific Applications:

• Structure–function relationships: Relates tunnel geometry and physico-chemical features to protein function and transport mechanisms.
• Inhibitor design and biocatalyst improvement: Informs design of inhibitors and engineering of biocatalysts by revealing structural determinants of molecular transport.
• Molecular dynamics analysis: Enables analysis of MD simulations to detect and quantify pathways, including applications such as studies on haloalkane dehalogenase DhaA.

Methodology:

CAVER 3.0 accepts molecular dynamics simulation trajectories as input, implements clustering algorithms to analyze pathway ensembles, and outputs detailed characteristics and summary statistics describing the time evolution of individual pathways.