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PocketPicker specifications

Information


Unique identifier OMICS_04159
Name PocketPicker
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Computer skills Advanced
Stability No
Maintained No

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Publication for PocketPicker

PocketPicker in publications

 (15)
PMCID: 5788505
PMID: 29377793
DOI: 10.7554/eLife.31097.026

[…] family members or related domains; for the enzymes considered here, identical results would have been obtained by identifying the largest cavity on the structure, for example, by using program pocketpicker (). co-factors (as generated by prodrg server []), metal ions, and water molecules were included in the protein structure preparation where required for enzyme function (; ; ). the kegg […]

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

[…] [], 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 pockets [, ], cavities [–], and channels […]

PMCID: 4858652
PMID: 27151361
DOI: 10.1038/srep25119

[…] which inhibit signalling pathways in both, cancer and healthy cells., a binding site prediction approach was initially applied to the crystal structure of apo mia (pdb id: 1i1j) using the software pocketpicker. this approach allowed us to identify a unique binding pocket that comprises the following amino acid residues of human mia: k10, l11, c12, q15, e16, c17, s18, h19, c35, r36, f37, v48, […]

PMCID: 4535767
PMID: 26270486
DOI: 10.1371/journal.pone.0135246

[…] the n-terminal end of helix 1 (see ). this motion closes a “novel” binding pocket discussed below. a second important feature of the simulation is that helix 1 unfolds and refolds repeatedly., a pocketpicker [] analysis was conducted for the 15 cluster-centers found by the classical clustering of the 4,100 md snapshots (the default settings described in reference [] were used). large (≥ 100 […]

PMCID: 4414931
PMID: 25932051
DOI: 10.1186/s13321-015-0059-5

[…] methods focus mainly on the algorithmic side of the problem of finding concave pockets and clefts on the surface of a 3d structure. some methods are purely geometrical (ligsite [], ligsitecs [], pocketpicker []), while others make use of additional physico-chemical information like polarity or charge (moe sitefinder [], fpocket [])., the energy based methods build on the approximation […]


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PocketPicker institution(s)
Johann Wolfgang Goethe-Universität, Beilstein Endowed Chair for Cheminformatics, Institut für Organische Chemie und Chemische Biologie, Frankfurt am Main, Germany

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