PockDrug statistics

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Citations per year

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

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Protocols

PockDrug specifications

Information


Unique identifier OMICS_08355
Name PockDrug
Interface Web user interface
Restrictions to use None
Input data Pocket structure (a PDB format file listing the atom pocket coordinates), Protein structure (PDB code, PDB protein file, a file of PDB code list)
Computer skills Basic
Stability Stable
Maintained Yes

Maintainer


  • person_outline Anne-Claude Camproux

Publication for PockDrug

PockDrug citations

 (5)
library_books

Exploration of the effect of sequence variations located inside the binding pocket of HIV 1 and HIV 2 proteases

2018
Sci Rep
PMCID: 5893546
PMID: 29636521
DOI: 10.1038/s41598-018-24124-5

[…] could be explained by a different pocket ability to bind drug-like molecules, hereafter referred to as the pocket druggability, we computed the druggability score of each PR1 and PR2 pocket using the PockDrug webserver,. All PR pockets were predicted to be druggable, with a similar average high score (0.90 ± 0.09 and 0.95 ± 0.03 for PR1 and PR2, respectively; Student test p-value = 0.07). Thus, th […]

library_books

Guanylate binding protein 1 is a potential new therapeutic target for triple negative breast cancer

2017
BMC Cancer
PMCID: 5688804
PMID: 29115931
DOI: 10.1186/s12885-017-3726-2

[…] , the Mx proteins. GBP1 is clearly overexpressed in TNBC tissues (Fig. , left) and cell lines (Fig. , right) and has at least 5 possible binding pockets for drug interactions (Fig. ) as calculated by PockDrug []. Moreover, GBP1 protein level is also enhanced in TNBC compared to non-TNBC samples as evaluated by MS protein analysis (Fig. ). The preferentially higher expression of GBP1 in TNBC tissue […]

call_split

Identification of gefitinib off targets using a structure based systems biology approach; their validation with reverse docking and retrospective data mining

2016
Sci Rep
PMCID: 5032012
PMID: 27653775
DOI: 10.1038/srep33949
call_split See protocol

[…] The pockets of top 128 hits were estimated based on ligand proximity within a fixed distance threshold from the bound ligand. To extract the residues localized within threshold distance; “PockDrug-Server” (http://pockdrug.rpbs.univ-paris-diderot.fr) was used. The PDB files were uploaded on the server and “prox” method was selected to estimate the pocket using threshold distance at 4 Å. […]

library_books

Dynamic profile analysis to characterize dynamics driven allosteric sites in enzymes

2016
Biophys Physicobiol
PMCID: 5042162
PMID: 27924265
DOI: 10.2142/biophysico.13.0_117

[…] ΔMSFall shows the long-range effect of the ligand binding on MSF of all the residues. ζ defined by quantifies the reduction ratio of MSF. Finally we examined druggability of the generated models by PockDrug-Server, which can extract the binding pocket from a submitted protein-ligand model and predict the pocket druggability as probability []. […]

call_split

Receptor Activity modifying Proteins 2 and 3 Generate Adrenomedullin Receptor Subtypes with Distinct Molecular Properties*

2016
PMCID: 4882435
PMID: 27013657
DOI: 10.1074/jbc.M115.688218
call_split See protocol

[…] s been shown to perform well in GPCR loop modeling (); this refinement removed any bias introduced by the extensions. The final models were minimized using PLOP ().Druggability was assessed using the PockDrug (, ) and DoGSiteScorer Web servers (); pocket hull volumes (which include atoms within the druggable binding pockets) were also determined using PockDrug; distances were measured using the Py […]


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PockDrug institution(s)
INSERM, UMRS-973, MTi, Université Paris Diderot, Paris, France; Université Paris Diderot, Sorbonne Paris Cité, UMRS-973, MTi, Paris, France
PockDrug funding source(s)
INSERM, Université Paris Diderot UMRS-973, recurrent funding and the BIP:BIP project, “Investissement d'Avenir”, Agence National de la Recherche (ANR) grant

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