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GraBCas specifications

Information


Unique identifier OMICS_01674
Name GraBCas
Software type Package/Module
Interface Graphical user interface
Restrictions to use None
Operating system Unix/Linux
Programming languages Java
Computer skills Medium
Stability Stable
Maintained Yes

Versioning


No version available

Publication for GraBCas

GraBCas citations

 (11)
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Interferon regulatory factor 8 regulates caspase 1 expression to facilitate Epstein Barr virus reactivation in response to B cell receptor stimulation and chemical induction

2018
PLoS Pathog
PMCID: 5794192
PMID: 29357389
DOI: 10.1371/journal.ppat.1006868
call_split See protocol

[…] Potential caspase cleavage sites were searched for all the EBV protein sequences using PeptideCutter (http://web.expasy.org/peptide_cutter/) and the GraBCas software [,]. […]

library_books

The linear ubiquitin chain assembly complex regulates TRAIL‐induced gene activation and cell death

2017
PMCID: 5412822
PMID: 28258062
DOI: 10.15252/embj.201695699

[…] o the apparent molecular weight of the cleavage fragment(s) observed, we narrowed down the cleavage sites within a region spanning approximately amino acids 325–400 (Fig A and C). Within this region, GrabCas (Backes et al, ) predicted two potential caspase‐8 cleavage sites, D348 and D387. In K562 HOIP KO cells reconstituted with HOIP D348A, the higher N‐terminal fragment band was still detected wh […]

library_books

Caspase 1 Promotes Epstein Barr Virus Replication by Targeting the Large Tegument Protein Deneddylase to the Nucleus of Productively Infected Cells

2013
PLoS Pathog
PMCID: 3795028
PMID: 24130483
DOI: 10.1371/journal.ppat.1003664

[…] Putative caspase cleavage sites were searched in the BPLF1 amino acid sequence using the GraBCas software . Sites with the highest probability of cleavage were identified by setting the cut-off scores to >15. […]

library_books

PROSPER: An Integrated Feature Based Tool for Predicting Protease Substrate Cleavage Sites

2012
PLoS One
PMCID: 3510211
PMID: 23209700
DOI: 10.1371/journal.pone.0050300

[…] s. A second issue is that only PeptideCutter , PoPS and SitePrediction were implemented to model and predict substrate cleavage sites for more than one protease family. For instance, CasPredictor , GraBCas and Cascleave can only be used to predict cleavage sites of caspases/granzyme B, but it is not feasible to apply them to predict cleavage sites of other proteases. The third issue is how to […]

library_books

Prediction of Protein Cleavage Site with Feature Selection by Random Forest

2012
PLoS One
PMCID: 3445488
PMID: 23029276
DOI: 10.1371/journal.pone.0045854

[…] ctions of cleavage sites of the human proteasome , .Besides the three methods mentioned above, most other tools are proteinase specific, such as GPS-CCD for the prediction of calpain cleavage sites , GraBCas for the prediction of sites cleaved by granzyme B and caspases and CaSPredictor for caspase substrate prediction . Therefore, these tools are limited in applicability. In this work, we develo […]

library_books

Developing a powerful In Silico tool for the discovery of novel caspase 3 substrates: a preliminary screening of the human proteome

2012
BMC Bioinformatics
PMCID: 3324375
PMID: 22269041
DOI: 10.1186/1471-2105-13-14

[…] ing cleavage site scoring matrices (CSSM). PeptideCutter [] is another tool that was designed with the objective of predicting cleavage sites for a wide range of proteases including various caspases. GraBCas [] is a tool that uses a position specific scoring matrix for caspases 1-9 and granzyme B, based on substrate specificities that were determined by positional scanning of synthetic peptides. C […]

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GraBCas institution(s)
Department of Human Genetics, Medical School, University of Saarland Homburg/Saar, Germany; Center for Bioinformatics, University of Saarland, Saarbrücken, Germany
GraBCas funding source(s)
A grant of the Center of Bioinformatics/Saarbrücken supported by the Deutsche Forschungsgemeinschaft; a grant from the Deutsche Krebshilfe (10-1966-Me4)

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