An improved deep learning method for predicting DNA-binding proteins based on contextual features in amino acid sequences.

• Main Authors: Siquan Hu, Ruixiong Ma, Haiou Wang
• Format: Article
• Language: English
• Published: Public Library of Science (PLoS) 2019-01-01
• Series: PLoS ONE
• Online Access: https://doi.org/10.1371/journal.pone.0225317

As the number of known proteins has expanded, how to accurately identify DNA binding proteins has become a significant biological challenge. At present, various computational methods have been proposed to recognize DNA-binding proteins from only amino acid sequences, such as SVM, DNABP and CNN-RNN. However, these methods do not consider the context in amino acid sequences, which makes it difficult for them to adequately capture sequence features. In this study, a new method that coordinates a bidirectional long-term memory recurrent neural network and a convolutional neural network, called CNN-BiLSTM, is proposed to identify DNA binding proteins. The CNN-BiLSTM model can explore the potential contextual relationships of amino acid sequences and obtain more features than can traditional models. The experimental results show that the CNN-BiLSTM achieves a validation set prediction accuracy of 96.5%-7.8% higher than that of SVM, 9.6% higher than that of DNABP and 3.7% higher than that of CNN-RNN. After testing on 20,000 independent samples provided by UniProt that were not involved in model training, the accuracy of CNN-BiLSTM reached 94.5%-12% higher than that of SVM, 4.9% higher than that of DNABP and 4% higher than that of CNN-RNN. We visualized and compared the model training process of CNN-BiLSTM with that of CNN-RNN and found that the former is capable of better generalization from the training dataset, showing that CNN-BiLSTM has a wider range of adaptations to protein sequences. On the test set, CNN-BiLSTM has better credibility because its predicted scores are closer to the sample labels than are those of CNN-RNN. Therefore, the proposed CNN-BiLSTM is a more powerful method for identifying DNA-binding proteins.