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Tunnel extraction software tools | Protein structure data analysis

Tunnels are void pathways leading from a cavity buried in a protein core to the surrounding solvent.

CAVER
Desktop

CAVER

Provides rapid, accurate and fully automated calculation of tunnels and…

Provides rapid, accurate and fully automated calculation of tunnels and channels in static structures. The molecules amendable to analysis of CAVER include proteins, nucleic acids or inorganic…

MOLE
Desktop
Web

MOLE

A web-based interactive application for the analysis of access/egress paths to…

A web-based interactive application for the analysis of access/egress paths to interior molecular voids. MOLEonline 2.0 enables platform-independent, easy-to-use and interactive analyses of…

SLITHER
Web

SLITHER

A web server that can generate contiguous conformations of a molecule along a…

A web server that can generate contiguous conformations of a molecule along a curved tunnel inside a protein, and the binding free energy profile along the predicted channel pathway. SLITHER adopts…

3V
Desktop
Web

3V Voss Volume Voxelator

Extracts and comprehensively analyzes all the internal volumes from input RNA…

Extracts and comprehensively analyzes all the internal volumes from input RNA and protein structures. 3V rapidly finds internal volumes by taking the difference between two rolling-probe…

MolAxis
Desktop
Web

MolAxis

A tool for the identification of high clearance pathways or corridors which…

A tool for the identification of high clearance pathways or corridors which represent molecular channels in the complement space of proteins. MolAxis is extremely efficient because it samples the…

CCCPP
Desktop

CCCPP Computes Cavities, Channels, Pores and Pockets in proteins

Computes the void parts of the proteins, i.e. cavities, channels and pockets.…

Computes the void parts of the proteins, i.e. cavities, channels and pockets. The present approach is a variant of the alpha shapes method, with the advantage of taking into account the size and the…

KVFinder
Desktop

KVFinder

A highly versatile and easy-to-use tool for cavity prospection and spatial…

A highly versatile and easy-to-use tool for cavity prospection and spatial characterization. KVFinder is a geometrical-based method that has an innovative customization of the search space. It…

HOLLOW
Desktop

HOLLOW

A program that generates a "casting" of the interior volume of the…

A program that generates a "casting" of the interior volume of the protein as dummy atoms. The use of HOLLOW significantly simplifies the generation of channel surfaces, and other interior…

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