MUFold-BetaTurn: A Deep Dense Inception Network for Protein Beta-Turn Prediction

Abstract: Beta-turn prediction is useful in protein function studies and experimental design. Although recent approaches using machine-learning techniques such as SVM, neural networks, and K-NN have achieved good results for beta-turn pre-diction, there is still significant room for improvement. As previous predictors utilized features in a sliding window of 4-20 residues to capture interactions among sequentially neighboring residues, such feature engineering may result in incomplete or biased features, and neglect interactions among long-range residues. Deep neural networks provide a new opportunity to address these issues. Here, we proposed a deep dense inception network (DeepDIN) for beta-turn prediction, which takes advantages of the state-of-the-art deep neural network design of the DenseNet and the inception network. A test on a recent BT6376 benchmark shows that the DeepDIN outperformed the previous best BetaTPred3 significantly in both the overall prediction accuracy and the nine-type beta-turn classification. A tool, called MUFold-BetaTurn, was developed, which is the first beta-turn prediction tool utilizing deep neural networks. The tool can be downloaded at http://dslsrv8.cs.missouri.edu/~cf797/MUFoldBetaTurn/download.html.