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Protocols

fpocket specifications

Information


Unique identifier OMICS_04153
Name fpocket
Interface Web user interface
Restrictions to use None
Computer skills Basic
Stability Stable
Maintained Yes

Maintainer


  • person_outline Pierre Tufféry

Publications for fpocket

fpocket citations

 (65)
library_books

A computational study for rational HIV 1 non nucleoside reverse transcriptase inhibitor selection and the discovery of novel allosteric pockets for inhibitor design

2018
Biosci Rep
PMCID: 5835713
PMID: 29437904
DOI: 10.1042/BSR20171113

[…] (iv) structural deviation caused by the mutations. Each vector was defined as below: NNRTIs binding pocket volume: Using ‘dpocket-pocket descriptor extraction’ in the protein cavity detection package fpocket [], the drug-binding pocket volume was estimated for each modeled RT–NNRTI mutant complex structure. Default parameters were used.Allosteric communication of the mutations to the DNA-binding p […]

call_split

Robust water desalination membranes against degradation using high loads of carbon nanotubes

2018
Sci Rep
PMCID: 5807517
PMID: 29426871
DOI: 10.1038/s41598-018-21192-5
call_split See protocol

[…] CNT was triple-walled [(15,15) > (10,10) > (5,5)] with a total of 2520 carbon atoms. Additionally, free volume (voids) determinations within the relaxed PA and CNT-PA cells were carried out with the Fpocket code, using probe spheres between 3.0 and 6.0 Å, 50 spheres as minimum clustering, and 4 neighboring spheres as interclustering criteria for free volume detection. Finally, 2D maps of potentia […]

library_books

Identification of allosteric inhibitors of the ecto 5' nucleotidase (CD73) targeting the dimer interface

2018
PLoS Comput Biol
PMCID: 5805337
PMID: 29377887
DOI: 10.1371/journal.pcbi.1005943

[…] The overall strategy followed in this study for cavity selection and hit identification is schematically illustrated in . First by analyzing the crystal structure (4H2G) and by using the Fpocket program, we detected five potential druggable cavities (). For the selection of the most suitable cavity, these pockets must fulfill important criteria: i) a cavity located far away from the s […]

library_books

Identification of New Potential APE1 Inhibitors by Pharmacophore Modeling and Molecular Docking

2017
PMCID: 5769857
PMID: 29307141
DOI: 10.5808/GI.2017.15.4.147

[…] itize the hits of the pharmacophore screen, we docked the hits against previously determined structures of APE1 [] (PDB ID: 1DEW) using AutoDock Vina []. A binding site of APE1 was assigned using the fpocket algorithm []. […]

library_books

Pockets as structural descriptors of EGFR kinase conformations

2017
PLoS One
PMCID: 5724837
PMID: 29228029
DOI: 10.1371/journal.pone.0189147

[…] Pockets, cavities and tunnels predictions on active and inactive conformers were performed using Fpocket program []. Pockets related to the active site of the kinase domain, the main pocket, were manually selected by visual inspection of the active conformers PDB ids 1M14 (apo form) and 2GS6, and […]

library_books

Insights from the protein protein interaction network analysis of Mycobacterium tuberculosis toxin antitoxin systems

2017
Bioinformation
PMCID: 5712783
PMID: 29225431
DOI: 10.6026/97320630013380

[…] Metapocket 2.0 was employed to determine active site of VapC9 and VapC10 []. Metapocket uses consensus approach to detect ligand-binding sites by employing eight methods: LIGSITE, PASS, SURFNET, Fpocket, GHECOM, ConCavity, POC ASA and Q-Sitefinder. […]

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fpocket institution(s)
Institucio Catalana de Recerca i Estudis Avancats (ICREA), Institut de Biomedicina de la Universitat de Barcelona (IBUB), Barcelona, Spain

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