Pocket-Finder specifications

Information


Unique identifier OMICS_17038
Name Pocket-Finder
Interface Web user interface
Restrictions to use Academic or non-commercial use
Computer skills Basic
Stability No
Maintained No

Subtools


  • behavr
  • damr
  • ggetho
  • scopr
  • sleepr
  • zeitgebr

Maintainers


This tool is not available anymore.

Additional information


https://rethomics.github.io/

Publications for Pocket-Finder

Pocket-Finder in publications

 (8)
PMCID: 5584760
PMID: 28873466
DOI: 10.1371/journal.pone.0183060

[…] [,]. the model was further validated by whatcheck (). the ramachandran plot for 3d structure of melf was also drawn (). the validated structure was used to identify a druggable pocket/site using pocket-finder, q-site finder [] and incasitefinder []. the top-scoring pockets were scrutinized to identify a pocket with better druggability index. one such pocket on melf was shortlisted […]

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

[…] and sequence to identify areas with functional activity., over the years, several techniques based on the third approach have been developed. these techniques include ligsite [], pocket [], pocket-finder [], surfnet [], cast [], pass [], cavity search [], voidoo [], apropos [], ligandfit [], 3dligandsite [], mspocket [], fpocket [], mcvol [], ghecom [], pocketdepth [], pocketpicker [], […]

PMCID: 4569619
PMID: 28324524
DOI: 10.1007/s13205-014-0274-1

[…] the templates used in protein modeling to identify the catalytic residues in hps. furthermore, active pocket sites in the predicted structures of hps were identified using pocasa (yu et al. ) and pocket-finder (laurie and jackson, ) servers. the ppm server (lomize et al. ) was used for calculating spatial positions in membranes of hps. the profunc (laskowski et al. ) web server was used […]

PMCID: 4243142
PMID: 25573232
DOI: 10.1186/1471-2164-15-S7-S3

[…] is documented. though the dogsitescorer predicts the druggable protein cavities, the host homologous proteins were further subjected to castp (computed atlas of surface topography of proteins) [], pocket-finder and q-sitefinder [] to get more reliable and robust results about the druggable cavities of the target proteins., 3d structure information and druggability analyses are important […]

PMCID: 4112621
PMID: 25038637
DOI: 10.1186/1472-6807-14-18

[…] space in a grid and identifies clefts by scanning areas that are enclosed on both sides by the protein’s atoms. an alpha-shape algorithm is used by cast [] and apropos []. drugsite [] and pocket-finder [], in addition to the protein’s shape, also consider physicochemical properties for identification of ligand binding pockets. further geometrical algorithms are travel depth [], voidoo […]


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Pocket-Finder institution(s)
Department of Life Sciences, Imperial College London, London, UK; Institute for Neuro- and Behavioral Biology, Westfalische Wilhelms University, Munster, Germany

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