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Volume calculation software tools | Protein structure data analysis

The molecular surface volume is a useful metric that describes contribution of geometrical volume, which includes van der Waals volume and volume of the voids, to the total volume of a protein in solution, thus isolating the effects of hydration for…
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…

Depth
Web

Depth

Accurately computes depth and solvent-accessible surface area (SASA) values.…

Accurately computes depth and solvent-accessible surface area (SASA) values. Depth is useful for all structural analysis based on residue depth and SASA, such as guiding site-directed mutagenesis…

POVME
Desktop

POVME POcket Volume Measurer

Allows users to extract actionable information from ensembles of protein…

Allows users to extract actionable information from ensembles of protein structures. POVME is a binding pocket analysis software that performs pocket selection for ensemble docking and provides…

Voronoia
Desktop
Web

Voronoia

A program suite to analyse and visualize the atomic packing of protein…

A program suite to analyse and visualize the atomic packing of protein structures. Voronoia is based on the Voronoi Cell method and can be used to estimate the quality of a protein structure, e.g. by…

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…

ProteinVolume
Desktop
Web

ProteinVolume

A highly robust and easy-to-use tool to compute geometric volumes of proteins.…

A highly robust and easy-to-use tool to compute geometric volumes of proteins. ProteinVolume generates the molecular surface of a protein and uses an innovative flood-fill algorithm to calculate the…

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…

AVP
Desktop

AVP Another Void Program

A method for the analysis of voids in proteins and packing quality in a single…

A method for the analysis of voids in proteins and packing quality in a single united program. Traditionally been analysed using different approaches, but in reality they are extremes of the same…

Volarea
Desktop

Volarea

Allows for a rapid and fully automated analysis of molecular structures. The…

Allows for a rapid and fully automated analysis of molecular structures. The software calculates the surface area and the volume of molecular structures, as well as the volume of molecular cavities.…

McVol
Desktop

McVol

A Monte Carlo method for determining the volume of a molecule. McVol is also…

A Monte Carlo method for determining the volume of a molecule. McVol is also able to identify internal cavities as well as surface clefts und fill these cavities with water molecules.

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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