MusiteDeep provides a deep-learning method for general and kinase-specific phosphorylation site prediction. It is implemented by deep learning library Keras and Theano backend (the Keras2.0 and Tensorflow backend implementation were also provided under folder MusiteDeep_Keras2.0). At present, MusiteDeep only provides prediction of human phosphorylation sites; however, it also provides customized model training that enables users to train other PTM prediction models by using their own training data sets based on either CPU or GPU.