GraBCas: a bioinformatics tool for score-based prediction of Caspase- and Granzyme B-cleavage sites in protein sequences.
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.
Backes
Christina
C
Department of Human Genetics Building 60 Medical School, University of Saarland, 66421 Homburg/Saar, Germany.
Kuentzer
Jan
J
Lenhof
Hans-Peter
HP
Comtesse
Nicole
N
Meese
Eckart
E
D020169:Caspases / Q000378:metabolism*; D019295:Computational Biology / Q000379:methods*; D053804:Granzymes; D020407:Internet; D020539:Sequence Analysis, Protein / Q000379:methods*; D012697:Serine Endopeptidases / Q000378:metabolism*; D012984:Software; D013379:Substrate Specificity
D053804:Granzymes; D012697:Serine Endopeptidases; D020169:Caspases