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Cavity extraction software tools | Protein structure data analysis

A cavity is a void in a molecular interior that is not accessible to bulk solvent around the molecule and can be either hydrated or free from any solvent molecule.

BetaCavityWeb
Web

BetaCavityWeb

Molecular cavities, which include voids and channels, are critical for…

Molecular cavities, which include voids and channels, are critical for molecular function. BetaCavityWeb computes these cavities for a given molecular structure and a given spherical probe, and…

CASTp
Web

CASTp

An online tool that locates and measures pockets and voids on 3D protein…

An online tool that locates and measures pockets and voids on 3D protein structures. CASTp includes annotated functional information of specific residues on the protein structure. The annotations are…

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…

PrinCCes
Desktop

PrinCCes Protein internal Channel & Cavity estimation

A computer program supporting the visualization of voids. PrinCCes includes a…

A computer program supporting the visualization of voids. PrinCCes includes a novel algorithm for the decomposition of the entire void volume of the protein or protein complex to individual entities.…

RosettaHoles
Desktop

RosettaHoles

A method for visual and quantitative assessment of underpacking in the protein…

A method for visual and quantitative assessment of underpacking in the protein core. RosettaHoles generates a set of spherical cavity balls that fill the empty volume between atoms in the protein…

BetaVoid
Desktop

BetaVoid

Recognizes molecular voids in the van der Waals surface or the Lee-Richards…

Recognizes molecular voids in the van der Waals surface or the Lee-Richards (solvent accessible) surface and computes their mass properties such the volume and the boundary area. Because BetaVoid is…

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…

SURFNET
Desktop

SURFNET

Generates molecular surfaces and gaps between surfaces from 3D coordinates…

Generates molecular surfaces and gaps between surfaces from 3D coordinates supplied in a PDB-format file. The gap regions can correspond to the voids between two or more molecules, or to the internal…

VOIDOO
Desktop

VOIDOO

A program for detection of cavities in macromolecular structures. It uses an…

A program for detection of cavities in macromolecular structures. It uses an algorithm that makes it possible to detect even certain types of cavities that are connected to "the outside…

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