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Protocols

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 citations

 (37)
library_books

Comparative systems analysis of the secretome of the opportunistic pathogen Aspergillus fumigatus and other Aspergillus species

2018
Sci Rep
PMCID: 5919931
PMID: 29700415
DOI: 10.1038/s41598-018-25016-4

[…] and is prepared for molecular docking using the prepare_ligand4.py script from AutoDockTools.Firstly, three ligand binding pockets for each filtered protein in A. fumigatus Af293 were predicted using metaPocket 2.0 (http://projects.biotec.tu-dresden.de/metapocket/). Secondly, for docking drugs to the predicted protein pockets, both protein and drug molecule were prepared by adding explicit hydroge […]

library_books

CD22 Binding Synthetic Sialosides Regulate B Lymphocyte Proliferation Through CD22 Ligand Dependent and Independent Pathways, and Enhance Antibody Production in Mice

2018
Front Immunol
PMCID: 5917077
PMID: 29725338
DOI: 10.3389/fimmu.2018.00820

[…] CD22 (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 with GSC839 […]

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

[…] ssessed by various structural assessment reports such as PROCHECK of swiss model server, ERRAT, ProSA-web, ProQ, MOLPROBITY and ResProx. In addition, active site of VapC9 and VapC10 was identified by Metapocket v2.0. The generated homology models and active site determined by metapocket v2.0 of VapC9 and VapC10, respectively are shown (, ). The developed models can be used for structure based drug […]

call_split

The Combined Use of in Silico, in Vitro, and in Vivo Analyses to Assess Anti cancerous Potential of a Bioactive Compound from Cyanobacterium Nostoc sp. MGL001

2017
Front Pharmacol
PMCID: 5711831
PMID: 29230175
DOI: 10.3389/fphar.2017.00873
call_split See protocol

[…] ion 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 Scientific […]

call_split

Active phytochemicals of Pueraria tuberosa for DPP IV inhibition: in silico and experimental approach

2017
PMCID: 5697100
PMID: 29201861
DOI: 10.1186/s40200-017-0328-0
call_split See protocol

[…] zing protein model geometry and removing ligands and other heteroatoms using the Discovery Studio 3.0. Further, the protein models were taken for active site prediction using Discovery Studio 3.0 and MetaPocket (http://projects.biotec.tu-dresden.de/metapocket/) [] and subjected to docking studies. Molecular docking calculation was done using the YASARA software []. For this, 25 selected phytochemi […]

library_books

NSiteMatch: Prediction of Binding Sites of Nucleotides by Identifying the Structure Similarity of Local Surface Patches

2017
PMCID: 5547728
PMID: 28811833
DOI: 10.1155/2017/5471607

[…] dues that were predicted as the binding residues, and FN (false negatives) are the binding residues that were predicted as the nonbinding residues.The NSiteMatch method is compared with the Findsite, MetaPocket, and Q-SiteFinder on three benchmark datasets that concern ADP-protein, ATP-protein, and AMP-protein interactions, respectively. The NSiteMatch and Findsite are template-based methods and t […]

Citations

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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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Anonymous user #106976

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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.