PockDrug statistics

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Associated diseases

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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 in publications

 (5)
PMCID: 5893546
PMID: 29636521
DOI: 10.1038/s41598-018-24124-5

[…] 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, […]

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

[…] 10, 2016. interaction network, structural information, structural druggable criteria and druggability rankings was assessed using the cansar [] database. structural drug pockets were assessed using pockdrug []., the ratio of the methylated probe intensity and the overall intensity (sum of methylated and unmethylated probe intensities), or beta value, were obtained from the humanmethylation450 […]

PMCID: 5032012
PMID: 27653775
DOI: 10.1038/srep33949

[…] of less than 0.5 (). since all the identified-pockets were from the crystal structure and have at least one bound ligand, the predicated druggability value of less than 0.5 could not be ignored. the pockdrug server also calculated 66 physicochemical properties (such as hydrophobicity, polarity, aromaticity etc.) of the pockets and the selected parameters are shown in . the binding pocket volumes […]

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 []., for the 10 selected structures, 101 complex models […]

PMCID: 4882435
PMID: 27013657
DOI: 10.1074/jbc.M115.688218

[…] 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 […]


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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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