Uppsala Software Factory - VOIDOO Package

Uppsala Software Factory - VOIDOO Package

Manuals

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

Related freebies

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make_surface.omac, an O macro that will generate and draw a solvent-accessible surface; uses surface.csh and VOIDOO
make_vdwsurf.omac, an O macro that will generate and draw a van der Waals surface; uses surface.csh and VOIDOO
merge_cavities.csh, script to merge multiple cavities found by VOIDOO into one map file
cavity.csh, script to run VOIDOO to find cavities
surface.csh, script to run VOIDOO to generate the solvent-accessible surface; mappage the surface with MAPMAN
Tutorial: Visualisation of tunnels. This explains how to visualise tunnels and other cavities in your protein that are connected to the outside world. The tutorial uses only Uppsala programs (MOLEMAN2, VOIDOO, MAMA, MAPMAN, and O).

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)

Requirements

VOIDOO is available for SGI, DEC ALPHA, LINUX and OSX systems. 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, JY Zou, M Kjeldgaard & TA Jones. International Tables for Crystallography, Volume F. Chapter 17.1, pp. 353-356, 366-367 (2001).
GJ Kleywegt & TA Jones, Acta Cryst., D50, 178-185 (1994).

Latest update at 20 September, 2002.