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

English version

Autoři: Siquan Hu ^aff001; Ruixiong Ma ^aff001; Haiou Wang ^aff003
Působiště autorů: School of Computer and Communication Engineering, University of Science and Technology Beijing, Beijing, China ^aff001; Sichuan Jiuzhou Video Technology Co., Ltd, Mianyang, China ^aff002; School of Chemistry and Biological Engineering, University of Science and Technology Beijing, Beijing, China ^aff003
Vyšlo v časopise: PLoS ONE 14(11)
Kategorie: Research Article
doi: https://doi.org/10.1371/journal.pone.0225317

Souhrn

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.

Klíčová slova:

Deep learning – DNA-binding proteins – Machine learning – Machine learning algorithms – Protein sequencing – Protein structure prediction – Recurrent neural networks – Support vector machines

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

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