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Posttranslational modification (PTM) plays key roles in many cellular processes such as signaling, cellular differentiation, protein degradation, protein stability, gene expression regulation, protein function regulation, and protein interactions. It has been estimated that there are more than 200 types of PTMs mediated by enzymes consisting of 5% of the proteome. PTM site prediction is a binary classification problem. Musite framework was designed for PTM site prediction in three processes: (i) data collection and preparation, (ii) feature extraction, and (iii) classifier/prediction model training and evaluation. With its GNU GPL open-source license and extensible API, Musite provides an open framework for PTM site prediction applications. The Musite framework contains six core modules. The authors provide standalone and web server versions of Musite, both with intuitive graphical user interface (GUI) to access the prediction models that they trained.