Computational prediction of MoRFs based on protein sequences and minimax probability machine

BACKGROUND: Molecular recognition features (MoRFs) are one important type of disordered segments that can promote specific protein-protein interactions. They are located within longer intrinsically disordered regions (IDRs), and undergo disorder-to-order transitions upon binding to their interaction partners. The functional importance of MoRFs and the limitation of experimental identification make it necessary to predict MoRFs accurately with computational methods. RESULTS: In this study, a new sequence-based method, named as MoRF(MPM), is proposed for predicting MoRFs. MoRF(MPM) uses minimax probability machine (MPM) to predict MoRFs based on 16 features and 3 different windows, which neither relying on other predictors nor calculating the properties of the surrounding regions of MoRFs separately. Comparing with ANCHOR, MoRFpred and MoRF(CHiBi) on the same test sets, MoRF(MPM) not only obtains higher AUC, but also obtains higher TPR at low FPR. CONCLUSIONS: The features used in MoRF(MPM) can effectively predict MoRFs, especially after preprocessing. Besides, MoRF(MPM) uses a linear classification algorithm and does not rely on results of other predictors which makes it accessible and repeatable.