Hjerrild, Majbrit3; Stensballe, Allan3; Rasmussen, Thomas E3; Kofoed, Christine B3; Blom, Nikolaj3; Sicheritz-Ponten, Thomas3; Larsen, Martin Røssel5; Brunak, Søren3; Jensen, Ole N6; Gammeltoft, Steen3
1 Faculty of Science, SDU2 Department of Biochemistry and Molecular Biology, Faculty of Science, SDU3 unknown4 Acute Medicine, Department of Clinical Research, Det Sundhedsvidenskabelige Fakultet, SDU5 Department of Biochemistry and Molecular Biology, Faculty of Science, SDU6 Acute Medicine, Department of Clinical Research, Det Sundhedsvidenskabelige Fakultet, SDU
Protein phosphorylation plays a key role in cell regulation and identification of phosphorylation sites is important for understanding their functional significance. Here, we present an artificial neural network algorithm: NetPhosK (http://www.cbs.dtu.dk/services/NetPhosK/) that predicts protein kinase A (PKA) phosphorylation sites. The neural network was trained with a positive set of 258 experimentally verified PKA phosphorylation sites. The predictions by NetPhosK were validated using four novel PKA substrates: Necdin, RFX5, En-2, and Wee 1. The four proteins were phosphorylated by PKA in vitro and 13 PKA phosphorylation sites were identified by mass spectrometry. NetPhosK was 100% sensitive and 41% specific in predicting PKA sites in the four proteins. These results demonstrate the potential of using integrated computational and experimental methods for detailed investigations of the phosphoproteome.
Journal of Proteome Research, 2011, Vol 3, Issue 3, p. 426-33