GPS-CCD statistics

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Number of citations per year for the bioinformatics software tool GPS-CCD
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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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Versioning


No version available

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 citations

 (8)
library_books

Investigating regulatory signatures of human autophagy related gene 5 (ATG5) through functional in silico analysis

2016
PMCID: 5006144
PMID: 27617225
DOI: 10.1016/j.mgene.2016.07.012

[…] is the most crucial post-translational modification (PTMs) of proteins that play an important role in many biological processes like cell death/apoptosis, cytoskeletal remodeling, and the cell cycle. GPS-CCD 1.0 tool was utilized for the prediction of calpain-cleavage sites in ATG5. Calpain mediated cleavage of ATG5 switches autophagy to apoptosis establishing important link between autophagy and […]

library_books

Calpain inhibition rescues troponin T3 fragmentation, increases Cav1.1, and enhances skeletal muscle force in aging sedentary mice

2016
Aging Cell
PMCID: 4854922
PMID: 26892246
DOI: 10.1111/acel.12453

[…] to the protein ladder. Figure S2B shows mass spectrometry analysis of trimethoxyphenyl phosphonium (TMPP)‐labeled nuclear protein extracts. TMPP‐labeled TnT3 N‐terminal amino acids are shown in red. GPS‐CCD 1.0 (Liu et al., ) indicates that two of three of the TMPP‐labeled sites are calpain cleavage sites. […]

library_books

Calpain 3 mediated regulation of the Na+ Ca2+ exchanger isoform 3

2015
PMCID: 4713461
PMID: 26503425
DOI: 10.1007/s00424-015-1747-8

[…] he data recorded in Figs. , , and clearly demonstrated that NCX3-AC activity is regulated by different calpains. Additionally, one of the cleavage sites for calpain predicted by the software program GPS-CCD 1.0 [] is located in the exon C of NCX3-AC, between the Leu-601 and Leu-602 (Fig. ). Next, exon C was removed by site-directed mutagenesis. The mutant NCX3-A had a significantly lower Ca2+ upt […]

library_books

Development of a neuroprotective peptide that preserves survival pathways by preventing Kidins220/ARMS calpain processing induced by excitotoxicity

2015
PMCID: 4632323
PMID: 26492372
DOI: 10.1038/cddis.2015.307

[…] n 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 were com […]

library_books

Calpain mediated cleavage of DARPP 32 in Alzheimer’s disease

2015
Aging Cell
PMCID: 4568975
PMID: 26178297
DOI: 10.1111/acel.12374

[…] e reaction 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 […]

library_books

Calpain Mediated Degradation of Drebrin by Excitotoxicity In vitro and In vivo

2015
PLoS One
PMCID: 4408054
PMID: 25905636
DOI: 10.1371/journal.pone.0125119

[…] e in NMDA-treated cultured neurons () and ischemic brain sections (), suggesting that drebrin A is a direct target of calpain both in vitro and in vivo. A bioinformatics search of drebrin A using the GPS-CCD package [] did not uncover any obvious potential calpain cleavage sites. This result is complicated further by the anomalous migration of drebrin on SDS-PAGE gels. In future studies, the actua […]


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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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