论文标题
深入学习蛋白质界面预测的高阶相互作用
Deep Learning of High-Order Interactions for Protein Interface Prediction
论文作者
论文摘要
蛋白质相互作用在广泛的生物过程中很重要。传统上,已经开发了计算方法来自动从手工制作的特征预测蛋白质界面。最近的方法采用了深层神经网络,并独立预测每种氨基酸对的相互作用。但是,这些方法不包含来自氨基酸链和高阶成对相互作用的重要顺序信息。直观地,氨基酸对的预测应取决于其特征和其他氨基酸对的信息。在这项工作中,我们建议将蛋白质界面预测作为2D密集的预测问题。此外,我们提出了一个新型的深层模型,以结合顺序信息和高阶成对相互作用以执行界面预测。我们表示蛋白质作为图形,并采用图形神经网络来学习节点特征。然后,我们提出了顺序建模方法,以结合顺序信息并重新排序特征矩阵。接下来,我们结合了高阶成对相互作用,以生成包含不同成对相互作用的3D张量。最后,我们采用卷积神经网络来执行2D密集的预测。对多个基准测试的实验结果表明,我们提出的方法可以始终如一地改善蛋白质界面预测性能。
Protein interactions are important in a broad range of biological processes. Traditionally, computational methods have been developed to automatically predict protein interface from hand-crafted features. Recent approaches employ deep neural networks and predict the interaction of each amino acid pair independently. However, these methods do not incorporate the important sequential information from amino acid chains and the high-order pairwise interactions. Intuitively, the prediction of an amino acid pair should depend on both their features and the information of other amino acid pairs. In this work, we propose to formulate the protein interface prediction as a 2D dense prediction problem. In addition, we propose a novel deep model to incorporate the sequential information and high-order pairwise interactions to perform interface predictions. We represent proteins as graphs and employ graph neural networks to learn node features. Then we propose the sequential modeling method to incorporate the sequential information and reorder the feature matrix. Next, we incorporate high-order pairwise interactions to generate a 3D tensor containing different pairwise interactions. Finally, we employ convolutional neural networks to perform 2D dense predictions. Experimental results on multiple benchmarks demonstrate that our proposed method can consistently improve the protein interface prediction performance.