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Using Deep learning method (CNN/RNN) for prediction of ubiquitination protein


Chunhui Xu






2206A Student Center

Ubiquitination, as a post-translational modification, is a crucial biological process presented in cell signaling, death and localization. Identification of ubiquitination protein is of fundamental importance for understanding molecular mechanisms in biological systems and diseases. Although high-throughput experimental studies using mass spectrometry have identified many ubiquitination proteins and ubiquitination sites, the vast majority of ubiquitination proteins remain undiscovered, even in well studied model organisms. To reduce experimental costs, computational (in silico) methods have been introduced to predict ubiquitination sites. If we can predict whether a query protein can be ubiquitinated or not, it is meaningful by itself and helpful for predicting ubiquitination sites. However, all the computational methods so far only predict ubiquitination sites, with unsatisfactory accuracy. In this study, we developed the deep learning method with CNN/RNN architecture in Pytorch environment for predicting ubiquitination proteins without relying on ubiquitination site prediction.