metaPocket statistics

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Associated diseases

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metaPocket specifications

Information


Unique identifier OMICS_04162
Name metaPocket
Alternative names MPK2, POCKET
Interface Web user interface
Restrictions to use None
Input format PDB
Output data The prediction results from eight single methods and the meta-pocket sites of MPK2 based on those results.
Output format PDB
Computer skills Basic
Version 2.0
Stability Stable
Maintained No

Maintainer


This tool is not available anymore.

Additional information


http://projects.biotec.tu-dresden.de/metapocket/help.php

Publications for metaPocket

metaPocket in publications

 (25)
PMCID: 5919931
PMID: 29700415
DOI: 10.1038/s41598-018-25016-4

[…] targets, the proteins were subsequently tested whether they could bind to their respective drugs (table ; methods). the four proteins were analyzed for the presence of ligand binding pockets using metapocket 2.0. for each of the four proteins, the top three ligand binding pockets were tested for ligand binding affinity using autodock vina. table  lists the four aspergillus proteins, […]

PMCID: 5917077
PMID: 29725338
DOI: 10.3389/fimmu.2018.00820

[…] (figure a) show 53% identity. the overall structure of the obtained model of mouse cd22 (figure b) is quite similar to that of human cd22 (). we analyzed presence of potential binding pockets by metapocket 2.0 server (). no pockets are present around conserved arg130, which forms a salt bridge with the carboxylate group of sialic acid., next, we generated the model of cd22 complexed […]

PMCID: 5711831
PMID: 29230175
DOI: 10.3389/fphar.2017.00873

[…] of terminus of each proteins were not require to perform. again discovery studio version 3.1 software was used to remove heteroatom, water molecules, and ligands before docking (gao and huang, ). metapocket 2.0 was used for predicting the active site of a target protein (http://projects.biotec.tu-dresden.de/metapocket/; huang, ; zhang et al., ). an advanced docking tool, yet another […]

PMCID: 5325476
PMID: 28234935
DOI: 10.1371/journal.pone.0172217

[…] with lrp6, these two boxes could bind to the third pe pair of lrp6 even stronger than the corresponding lrp6-binding sites of dkk1. further confirmation was achieved by using meta pocket 2.0 (mpk2) web tool []. this server utilizes a consensus method in which the binding sites are predicted by eight different methods including ligsitecs, pass, q-site finder, surfnet, fpocket, ghecom, […]

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

[…] [], 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 [] using pure geometric characteristics, and do not require any prior knowledge of the ligand […]


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metaPocket institution(s)
Systems Biology Division, Zhejiang-California International NanoSystems Institute, Zhejiang University, Hangzhou, China; Bioinformatics Group, Biotechnology Center, Technical University of Dresden, Dresden, Germany
metaPocket funding source(s)
Supported by Ministry of Science and Technology (MOST) China international cooperation projects (grant no: 2008DFA11320) and EU 7th Framework Marie Curie Actions of International Research Staff Exchange Scheme (IRSES) project (grant no: 247097).

metaPocket review

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William Silva

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Web
It provides connection sites with considerable success, providing input files to other software such as Pymol, Chimera and Discovery Studio.