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Citations per year

Number of citations per year for the bioinformatics software tool McVol
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Tool usage distribution map

This map represents all the scientific publications referring to McVol per scientific context
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Protocols

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

Versioning


No version available

Maintainer


  • person_outline G. Matthias Ullmann

Publication for McVol

McVol citations

 (6)
library_books

Normal Modes Expose Active Sites in Enzymes

2016
PLoS Comput Biol
PMCID: 5225006
PMID: 28002427
DOI: 10.1371/journal.pcbi.1005293

[…] loped. 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 for pock […]

library_books

Computational methods in drug discovery

2016
Beilstein J Org Chem
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 []. […]

call_split

Structural basis for the dissociation of α synuclein fibrils triggered by pressure perturbation of the hydrophobic core

2016
Sci Rep
PMCID: 5128797
PMID: 27901101
DOI: 10.1038/srep37990
call_split See protocol

[…] 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 […]

library_books

High resolution neutron and X ray diffraction room temperature studies of an H FABP–oleic acid complex: study of the internal water cluster and ligand binding by a transferred multipolar electron density distribution

2016
PMCID: 4775160
PMID: 27006775
DOI: 10.1107/S2052252515024161

[…] ogen bonds are on average rather short, with a mean O⋯O distance of 2.83 Å, leading to a mean volume of 17.2 Å3 per water molecule inside the cavity (the cavity volume was calculated with the program McVol; Till & Ullmann, 2010). This can be compared with a van der Waals water molecule volume between 16 and 18 Å3 and an average volume of 30 Å3 for bulk water at 24°C. Therefore, the water molecules […]

call_split

Filling Up the Heme Pocket Stabilizes Apomyoglobin and Speeds Up Its Folding

2014
PMCID: 4065233
PMID: 24456280
DOI: 10.1021/jp412459z
call_split See protocol

[…] 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 w […]

library_books

Measuring the shapes of macromolecules – and why it matters

2013
Comput Struct Biotechnol J
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 of the biomolecules […]


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

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