CAVER

CAVER identifies and analyzes tunnels and channels in static and dynamic protein structures to characterize transport pathways for small molecules, ions, and water solvent.

Key Features:

• Tunnel and channel identification: Detects and analyzes tunnels and channels in static and dynamic protein structures.
• Ensemble analysis (CAVER 3.0): Performs automatic analysis of transport pathways across large ensembles of protein conformations (CAVER 3.0).
• Pathway calculation and clustering: Calculates transport pathways and applies clustering algorithms to group similar pathways.
• Geometric, physico-chemical and dynamic characterization: Computes pathway geometry, physico-chemical properties, and dynamic behavior.
• MD trajectory input and time-resolved statistics: Accepts molecular dynamics simulation trajectories and provides time-evolution characteristics and summary statistics for individual pathways.

Scientific Applications:

• Structure–function analysis: Maps transport pathways to support analysis of structure–function relationships in proteins.
• Inhibitor design: Informs design of inhibitors by revealing access routes and gating mechanisms.
• Biocatalyst engineering: Supports engineering of improved biocatalysts through identification and assessment of transport tunnels.
• Molecular transport and recognition studies: Characterizes access paths relevant to molecular transport, molecular recognition, and enzymatic catalysis.
• Tunnel gating investigation: Enables investigation of tunnel gating mechanisms and highlights the importance of molecular dynamics in estimating pathway characteristics.
• Case study — haloalkane dehalogenase DhaA: Identified and assessed all previously published tunnels in DhaA, including those closed in crystal structures.

Methodology:

Performs automatic analysis of transport pathways in large ensembles of protein conformations; calculates and clusters pathways using its algorithms; accepts molecular dynamics simulation trajectories and computes characteristics and summary statistics describing the time evolution of individual pathways.