Protein palmitoylation, also known as S-acylation, is one of the most ubiquitous post-translational modifications (PTM), reversibly attaching a 16-carbon saturated fatty acid as lipid palmitate (C16:0) to cysteine residues in protein substrates through thioester linkage (Bijlmakers and Marsh, 2003; Dietrich and Ungermann, 2004; el-Husseini Ael and Bredt, 2002; Linder and Deschenes, 2003; Smotrys and Linder, 2004; Huang and El-Husseini, 2005). Basically, palmitoylation increases the hydrophobicity of proteins to promote protein-membrane association. Also, palmitoylation modifies numerous proteins to control protein-protein interaction (Yang, et al., 2004; Zhou, et al., 2004; Clark, et al., 2004), intracellular trafficking (Kalinina, et al., 2003; Navarro-Lerida, et al., 2004), lipid rafts targeting (Salaun, et al., 2005; Wong and Schlichter, 2004), and proteins activities (Zhou, et al., 2004; Vazquez, et al., 2005), etc. Moreover, palmitoylation has been implicated in a variety of biological and physiological processes, including signal transduction (Vazquez, et al., 2005; Kleuss and Krause, 2003), mitosis (Caron, et al., 2001), neuronal development (el-Husseini Ael and Bredt, 2002; Huang and El-Husseini, 2005), and apoptosis (Wang and Sebti, 2005), etc. Although protein palmitoylation has attracted extensive attention, its molecular mechanisms still remain to be elusive.

    To date, only a few palmitoylation sites have been experimentally identified. Although several efficient techniques, such as mass spectrometry (MS), have been employed recently, most of the known palmitoylation sites are mapped by mutagenesis of candidate cysteine residues with conventional biochemical methods. The features of substrate specificity for palmitoylation is still unclear and most previous studies have proposed that there is no common and canonical consensus sequence/motif for palmitoylation (Bijlmakers and Marsh, 2003; el-Husseini Ael and Bredt, 2002; Smotrys and Linder, 2004). These intrinsic and disordered characteristics of palmitoylation introduce great difficulties into choosing appropriate candidate cysteine residues in the substrates for further experimental manipulation. Thus, in silico prediction of palmitoylation sites implemented in an apt algorithm/approach is in urgent need and insightful for the further experimental design.

    In this work, we present a computational web service of NBA-Palm - Prediction of Palmitoylation Site Implemented in Naive Bayesian Algorithm. The training data set includes 245 non-homologous sites from 105 proteins. The accuracy of NBA-Palm is 86.15% with the window length of seven. The prediction performance could be comparable with our previous work of CSS-Palm. Taken together, we propose the prediction results of NBA-Palm might be useful for further experimental consideration.