Locating apoptosis proteins by incorporating the signal peptide cleavage sites into the general form of Chou's Pseudo amino acid composition

Apoptosis proteins play an essential role in the development and homeostasis of an organism. The accurate prediction of subcellular location for apoptosis proteins is helpful for understanding the mechanism of programmed cell death and their biological functions. In this article, a new apoptosis proteins localization algorithm, named PSSP, is proposed based on the predicted cleavage sites of primary protein sequences. First, protein chains are divided into N‐terminal signal parts and mature protein parts according to their predicted cleavage sites by SignalP. Then, amino acid composition (ACC) of the individual subsequence together with pseudo‐ACC and stereochemical properties of whole chain were extracted to represent a given protein sequence. Jackknife test by support vector machine on three broadly used datasets (ZD98, ZW225, and CL317 datasets) of apoptosis proteins demonstrated that the total accuracies by this approach are 93.9, 87.6, and 91.5%, respectively. In addition, an independent nonapoptosis benchmark dataset (NNPSL) was also used to evaluate the performance of this method, and predictive accuracies for eukaryotic and prokaryotic proteins are also comparable to existing methods. © 2013 Wiley Periodicals, Inc.