Pripper: prediction of caspase cleavage sites from whole proteomes

Background: Caspases are a family of proteases that have central functions in programmed cell death (apoptosis) and inflammation. Caspases mediate their effects through aspartate-specific cleavage of their target proteins, and at present almost 400 caspase substrates are known. There are several methods developed to predict caspase cleavage sites from individual proteins, but currently none of them can be used to predict caspase cleavage sites from multiple proteins or entire proteomes, or to use several classifiers in combination. The possibility to create a database from predicted caspase cleavage products for the whole genome could significantly aid in identifying novel caspase targets from tandem mass spectrometry based proteomic experiments. Results: Three different pattern recognition classifiers were developed for predicting caspase cleavage sites from protein sequences. Evaluation of the classifiers with quality measures indicated that all of the three classifiers performed we...

• Type: Journal
• Year: 2010
• Where: BMCBI
• Authors: Mirva Piippo, Niina Lietzén, Olli Nevalainen, Jussi Salmi, Tuula A. Nyman
• Keywords: BMCBI 2010, Caspase, Caspase Cleavage, Caspase Cleavage Sites