DeepPPI: Boosting Prediction of Protein-Protein Interactions with Deep Neural Networks

作者：Du, Xiuquan^*; Sun, Shiwei; Hu, Changlin; Yao, Yu; Yan, Yuanting; Zhang, Yanping

来源：Journal of Chemical Information and Modeling, 2017, 57(6): 1499-1510.

DOI：10.1021/acs.jcim.7b00028

• AMINO-ACID-SEQUENCES
• SUBCELLULAR LOCATIONS
• HYPERPLANES
• ENSEMBLE
• AFFINITY
• DATABASE
• ORDER
• FOLD
• TOOL

The complex language,of eukaryotic gene expression remains incompletely understood. Despite the importance suggested by many proteins' variants statistically associated with human disease, nearly all such variants have unknown mechanisms, for example, protein protein interactions, (PPIs). In this study, we address this challenge using a recent Machine learning advance-deep neural networks (DNNs). We aim at improving the performance of PPIs prediction and propose a method called DeepPPI (Deep neural networks for Protein Protein Interactions prediction), which employs deep-neural: networks to learn effectively the representations of proteins from; common protein descriptors. The experimental results indicate that DeepPPI achieves superior performance on the test data set with an Accuracy of 92.50%, Precision of 94.38%, Recall of 90.56%, Specificity of 94.49%, Matthews correlation Coefficient of 85.08% and:Area Under the Curve of 97.43%, respectively. Extensive experiments show that DeepPPI can learn useful features of proteins pairs by a layer-wise abstraction, and thus achieves better prediction performance than existing methods. The source code of our approach, can be available via http://ailab.ahu.edu.cn:8087/DeepPPI/index.html.

• 出版日期2017-6
• 单位安徽大学