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GraBCas: a bioinformatics tool for score-based prediction of Caspase- and Granzyme B-cleavage sites in protein sequences

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GraBCas: a bioinformatics tool for score-based prediction of Caspase- and Granzyme B-cleavage sites in protein sequences

Auteurs : Christina Backes ; Jan Kuentzer [Allemagne] ; Hans-Peter Lenhof [Allemagne] ; Nicole Comtesse ; Eckart Meese

Source :

Nucleic Acids Research [ 0305-1048 ] ; 2005-07-01.

RBID : ISTEX:951BBB6B9A6A9C9DFB113220D9D7479EDCA26338

English descriptors

Teeft :
- Amino, Amino acid, Amino acid sequence, Amino acids, Apoptosis, Beta, Caspase, Catenin protein, Cell death, Cleavage, Cleavage site, Cleavage sites, Cutoff, Cutoff value, Cysteine, Fragmentation factor, Grabcas, Grabcas program, Granzyme, High variability, Kinase, Lter, Matrix, Nucleic acids research, Polypeptide, Potential cleavage sites, Protease, Protein kinase, Protein sequence analysis, Proteinase inhibitor, Server, Server issue, Stringency.

Abstract

Caspases and granzyme B are proteases that share the primary specificity to cleave at the carboxyl terminal of aspartate residues in their substrates. Both, caspases and granzyme B are enzymes that are involved in fundamental cellular processes and play a central role in apoptotic cell death. Although various targets are described, many substrates still await identification and many cleavage sites of known substrates are not identified or experimentally verified. A more comprehensive knowledge of caspase and granzyme B substrates is essential to understand the biological roles of these enzymes in more detail. The relatively high variability in cleavage site recognition sequence often complicates the identification of cleavage sites. As of yet there is no software available that allows identification of caspase and/or granzyme with cleavage sites differing from the consensus sequence. Here, we present a bioinformatics tool ‘GraBCas’ that provides score-based prediction of potential cleavage sites for the caspases 1–9 and granzyme B including an estimation of the fragment size. We tested GraBCas on already known substrates and showed its usefulness for protein sequence analysis. GraBCas is available at http://wwwalt.med-rz.uniklinik-saarland.de/med_fak/humangenetik/software/index.html.

Url:

https://api.istex.fr/document/951BBB6B9A6A9C9DFB113220D9D7479EDCA26338/fulltext/pdf

DOI: 10.1093/nar/gki433

Affiliations:

Allemagne

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Le document en format XML

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GraBCas: a bioinformatics tool for score-based prediction of Caspase- and Granzyme B-cleavage sites in protein sequences

GraBCas: a bioinformatics tool for score-based prediction of Caspase- and Granzyme B-cleavage sites in protein sequences

Source :

English descriptors

Abstract

Links toward previous steps (curation, corpus...)

Le document en format XML

Pour manipuler ce document sous Unix (Dilib)

Pour mettre un lien sur cette page dans le réseau Wicri