Uppsala Software Factory

Uppsala Software Factory - VOIDOO

Manuals

FLOOD to fill a cavity with water molecules
MAPROP to produce maps of various properties
VOIDOO to find cavities and analyse volumes

Description

VOIDOO is 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 world". Three different types of cavity can be handled by VOIDOO: Vanderwaals cavities (the complement of the molecular Vanderwaals surface), probe-accessible cavities (the cavity volume that can be occupied by the centres of probe atoms) and MS-like probe-occupied cavities (the volume that can be occupied by probe atoms, i.e. including their radii).

VOIDOO can be used for:

detecting and delineating cavities
measuring cavity volumes and molecular volumes
identifying non-protein atoms inside cavities
identifying protein atoms that line the surface of cavities
producing display files for O for visualising cavities
producing macro files for O to display (1) non-protein residues (ligands, solvent molecules) that are situated inside each cavity, and (2) protein residues that surround each cavity
producing display files for O for visualising molecular surfaces
(randomly) rotating molecules for assessing the accuracy of cavity volumes (by repeated calculations using differently oriented copies of a molecule)

Platforms

VOIDOO is available for SGI and DEC ALPHA/OSF1 workstations. Visualisation of cavities and molecular surfaces requires O. Several library files with Vanderwaals radii are provided, e.g. one with values taken from AMBER, the other with values to emulate Connolly's MS program. MAPROP comes with several precooked library files.

References

GJ Kleywegt & TA Jones, Acta Cryst., D50, 178-185 (1994).

Latest update at 6 February, 1999.