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GraBCas: a bioinformatics tool for score-based prediction of Caspase- and Granzyme B-cleavage sites in protein sequences
Department of Human Genetics Building 60 Medical School, University of Saarland 66421 Homburg/Saar, Germany 1Center for Bioinformatics Building 36.1 University of Saarland 66041 Saarbrücken, Germany
*To whom correspondence should be addressed. Tel: +49 6841 162 6038; Fax: +49 6841 162 6186; Email: hgemee{at}uniklinik-saarland.de
Received February 12, 2005. Revised March 24, 2005. Accepted March 24, 2005.
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.
The authors wish it to be known that, in their opinion, the last two authors should be regarded as joint First Authors
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