GPS-CCD statistics

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Associated diseases

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GPS-CCD specifications

Information


Unique identifier OMICS_01673
Name GPS-CCD
Alternative name Calpain Cleavage Detector
Software type Package/Module
Interface Graphical user interface
Restrictions to use Academic or non-commercial use
Operating system Unix/Linux, Mac OS, Windows
Programming languages Java
Computer skills Medium
Version 1.0
Stability Stable
Maintained Yes

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Documentation


Maintainers


  • person_outline Jian Ren <>
  • person_outline Yu Xue <>
  • person_outline Zexian Liu <>

Additional information


http://ccd.biocuckoo.org/faq.php

Information


Unique identifier OMICS_01673
Name GPS-CCD
Alternative name Calpain Cleavage Detector
Interface Application programming interface
Restrictions to use Academic or non-commercial use
Programming languages Java
Computer skills Advanced
Stability Stable
Maintained Yes

Documentation


Maintainers


  • person_outline Jian Ren <>
  • person_outline Yu Xue <>
  • person_outline Zexian Liu <>

Additional information


http://ccd.biocuckoo.org/faq.php

Publication for Calpain Cleavage Detector

GPS-CCD in publications

 (8)
PMCID: 5006144
PMID: 27617225
DOI: 10.1016/j.mgene.2016.07.012

[…] web server called bdm-pub (prediction of ubiquitination site with bayesian discriminant method; http://bdmpub.biocuckoo.org/) was used to predict ubiquitination sites. group-based prediction system-calpain cleavage detector (gps-ccd) 1.0 tool was utilized for the prediction of calpain-cleavage sites in atg5 ()., search tool for the retrieval of interacting genes/proteins-string database […]

PMCID: 4824854
PMID: 26796116
DOI: 10.1074/mcp.M115.053413

[…] (loo) accuracy of 74.9% (, versus p87 p6-p6′)., a importance was automatically calculated by the moe software., a abbreviations used, gps-h, -m, or -l: high-, medium-, or low-threshold mode of gps-ccd ver.1; svl-r or -l: support vector machine using rbf or linear kernels; pssm: position-specific scoring matrix method; mkl: multiple kernel learning method; sp-c1, or -c2: site prediction […]

PMCID: 4713461
PMID: 26503425
DOI: 10.1007/s00424-015-1747-8

[…] pcineo ires-gfp vectors with a ha-tag fused at the n-terminus of the protein has been previously described in detail []. calpain cleavage sites were predicted using the group base prediction system-calpain cleavage detector (gps-ccd) 1.0 prediction tool []. the variant-specific cleavage site was mutated using site-directed mutagenesis, performed on ncx3-ac leading to the following mutation: […]

PMCID: 4632323
PMID: 26492372
DOI: 10.1038/cddis.2015.307

[…] cleavage sites in rat kidins220 last c-terminal 1000 amino acids was performed using the online services provided by calpain modulatory proteolysis database (campdb; http://www.calpain.org) and gps-calpain cleavage detector (gps-ccd; http://ccd.biocuckoo.org). predictions from five different algorithms (linear or radial basis function kernel, pssm, mkl and gps 2.0) were run. the results […]

PMCID: 4568975
PMID: 26178297
DOI: 10.1111/acel.12374

[…] mixture was incubated with calpeptin, a calpain inhibitor, the cleavage product was not generated (fig.)., to identify the calpain cleavage site of darpp-32, we used a computational program (gps-ccd) (liu et al., ) that predicts potential cleavage sites. our earlier data showed that the larger endogenous darpp-32 cleavage product contained the thr34 residue (fig.) and that the n-terminal […]


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GPS-CCD institution(s)
Hefei National Laboratory for Physical Sciences at Microscale and School of Life Sciences, University of Science and Technology of China, Hefei, China; Hubei Bioinformatics and Molecular Imaging Key Laboratory, Department of Systems Biology, College of Life Science and Technology, Huazhong University of Science and Technology, Wuhan, Hubei, China; State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University (SYSU), Guangzhou, China
GPS-CCD funding source(s)
Supported by grants from the National Basic Research Program (973 project) (2010CB945400, 2011CB910400), National Natural Science Foundation of China (90919001, 31071154, 30900835, 30830036, 91019020, 21075045), and Fundamental Research Funds for the Central Universities (HUST: 2010JC049, 2010ZD018; SYSU: 11lgzd11, 11lgjc09).

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