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VOIDOO specifications

Information


Unique identifier OMICS_07910
Name VOIDOO
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS
Computer skills Advanced
Stability Stable
Maintained Yes

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Publication for VOIDOO

VOIDOO in publications

 (44)
PMCID: 5656587
PMID: 29070857
DOI: 10.1038/s41598-017-14101-9

[…] model of arabidopsis pyl2 (pdb code: 3kb0) as search model. coot was used to manually rebuild the structure model, and the structure was further refined using phenix software package. the program voidoo was used to determine the size of the aba-binding pocket. all the structure figures presented in this paper were prepared by using pymol (delano scientific). a summarized statistics of data […]

PMCID: 5436139
PMID: 28488697
DOI: 10.1038/ncomms15109

[…] in the crystal structure is d2 after schoenflies (222 after hermann-mauguin). the cavity volume was calculated to be 1,719 å3 (1.7 nm3) using a 3.0 å probe in the void space calculation using voidoo (). to prevent the probe from ‘escaping' the inner sphere through the large pores, the default probe radius of 1.4 å (water) was increased to 3.0 å. this results in smaller calculated volumes […]

PMCID: 5297245
PMID: 28176812
DOI: 10.1038/srep41751

[…] the volume of the detergent belt, vbelt can be approximated to the sum of the volume vdet occupied by each detergent molecule,, , vdet is calculated for a given detergent by using the program voidoo (http://xray.bmc.uu.se/usf/voidoo.html) (). the number of bound detergent molecules, n, is determined experimentally by maldi-tof ms., vbelt can also be approximated to a hollow cylinder […]

PMCID: 5225006
PMID: 28002427
DOI: 10.1371/journal.pcbi.1005293

[…] over the years, several techniques based on the third approach have been developed. these techniques include ligsite [], pocket [], pocket-finder [], surfnet [], cast [], pass [], cavity search [], voidoo [], apropos [], ligandfit [], 3dligandsite [], mspocket [], fpocket [], mcvol [], ghecom [], pocketdepth [], pocketpicker [], vice [], as well as consensus techniques which use a combination […]

PMCID: 4999047
PMID: 27095669
DOI: 10.1002/anie.201602135

[…] and equatorial compression in 2. although of similar areas (20–30 å2), the open triangular apertures of 2 resultantly present a less equilateral surface than 1. void volumes, calculated using voidoo, revealed cavities of 282 å3 for 1 and 423 å3 for 2. these volumes are approximately ten times larger than those of the mii 4l4 tetrahedra formed from the same triamines using […]


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VOIDOO institution(s)
Department of Molecular Biology, Biomedical Centre, University of Uppsala, Sweden

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