SiteSeek: Post-translational modification analysis using adaptive locality-effective kernel methods and new profiles

The performance of the proposed model was compared to nine existing different machine learning models and four widely known phosphorylation site predictors with the newly proposed PS-Benchmark_1 dataset to contrast their accuracy, sensitivity, specificity and correlation coefficient. SiteSeek showed better predictive performance with 86.6% accuracy, 83.8% sensitivity, 92.5% specificity and 0.77 correlation-coefficient on the four main kinase families (CDK, CK2, PKA, and PKC).Our newly proposed methods used in SiteSeek were shown to be useful for the identification of protein phosphorylation sites as it performed much better than widely known predictors on the newly built PS-Benchmark_1 dataset.Post-translational modifications are observed on almost all proteins analysed to date. During phosphorylation, a phosphate molecule is placed on another molecule resulting in the functional activation or inactivation of the receiving molecule. These modifications have a substantial influence on the structure and functions of protein. Phosphorylation at the serine, threonine and tyrosine residues by enzymes of the kinase and phosphatise super-families is one of the most frequent forms of post-translational modifications in intracellular proteins. As phosphorylation has a significant impact on diverse cellular signalling processes, it is needed in the regulation of cell differentiation, as a trigger for the progression of the cell cycle and control of metabolism, transcription, apoptosis, cytoskeletal rearrangements [1-7] in animals. As importantly, the phosphorylation of protein is considered as being a key event in many signal transduction pathways of biological systems [8]. It is thus important for us to be able to accurately determine the phosphorylation state of proteins so as to better identify the state of a cell.It has been widely reported in literature that a large number of human diseases are caused by a disruption of normal cellular phosphorylation events. For example