Phos3D is a web server for the prediction of phosphorylation sites (P-sites) in proteins. The approach is based on Support Vector Machines trained on sequence profiles enhanced by information from the spatial context of experimentally identified P-sites. In addition to serine, threonine, and tyrosine P-sites, Phos3D is capable to predict kinase-specific phosphorylations by the serine kinases PKA, PKC, MAPK, and CKII, as well as by the tyrosine kinase SRC. The quality of predictions is greatly dependent on the quality of submitted protein structures. Erroneous or incomplete protein structures may lead to inaccurate predictions.