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Associated diseases

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McVol specifications

Information


Unique identifier OMICS_07913
Name McVol
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
License GNU General Public License version 2.0
Computer skills Advanced
Stability Stable
Maintained Yes

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Maintainer


  • person_outline G. Matthias Ullmann <>

Publication for McVol

McVol in publications

 (5)
PMCID: 5225006
PMID: 28002427
DOI: 10.1371/journal.pcbi.1005293

[…] 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 thereof such as metapocket []. other methods analyze the protein surface […]

PMCID: 5238551
PMID: 28144341
DOI: 10.3762/bjoc.12.267

[…] ligands that are too bulky to fit in the pocket can be done during the lead identification process. one algorithm that calculates the volume of a binding pocket is povme (pocket volume measurer) []. mcvol is another standalone program that can identify and calculate the volume binding cavities in protein structures by using a monte carlo algorithm []., in molecular docking, how well a drug binds […]

PMCID: 5128797
PMID: 27901101
DOI: 10.1038/srep37990

[…]  μm α-syn monomers., internal cavities and surface clefts were mapped in the ssnmr structure of the α-syn fibril [protein data bank (pdb) id code 2n0a] based on the monte carlo method included in the mcvol suite. the applied algorithm used a probe sphere of 1.3 å, 50 monte carlo steps per å3 of the molecule, and 2,500 dots per atom on the dotted surface. the minimum volume for cavities to be consi […]

PMCID: 4065233
PMID: 24456280
DOI: 10.1021/jp412459z

[…] ns simulations were used and data was extracted one structure per nanosecond. van der waals radii for the atoms were assigned from the charmm27 force field using vmd. voids were identified using the mcvol software. mcvol uses a monte carlo approach in combination with a fine grid to classify points that are parts of the protein, solvent, or voids (cavity or cleft). protein surfaces were defined […]

PMCID: 3962087
PMID: 24688748
DOI: 10.5936/csbj.201309001

[…] the measures of these pockets (volume and surface area) are then computed by monte carlo integration over their corresponding grid points. pocket [], ligsite [], ligandfit [], pocketpicker [], and mcvol [] are cavity-detecting programs that implement this grid-based method., the probe sphere method proceeds by placing probe spheres that are tangent to the surfaces of two atoms […]


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McVol institution(s)
Structural Biology/Bioinformatics, University of Bayreuth, Bayreuth, Germany

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