基于卷积长短时记忆神经网络的蛋白质二级结构预测

鉴于不同类型氨基酸的相互作用对蛋白质结构预测的影响不同,文中融合卷积神经网络和长短时记忆神经网络模型,提出卷积长短时记忆神经网络,并应用到蛋白质8类二级结构的预测中.首先基于氨基酸序列的类别信息和氨基酸结构的进化信息表示蛋白质序列,并采用卷积提取氨基酸残基之间的局部相关特征,然后利用双向长短时记忆神经网络提取蛋白质序列内部残基之间的远程相互作用,最后将提取的蛋白质的局部相关特征和远程相互作用用于蛋白质8类二级结构的预测.实验表明,相比基准方法,文中模型提高8类二级结构预测的精度,并具有良好的可扩展性.

Protein Secondary Structure Prediction Based on Convolutional Long Short-Time Memory Neural Networks

Since the interaction of different types of amino acid has an influence on the prediction of protein structure, convolutional neural networks and long short-term memory neural networks are integrated. A convolutional long short-term memory neural network is proposed to predict 8-class protein secondary structures. Firstly, the protein sequence is represented based on the amino acid sequence class feature and the amino acid structure profile feature. The local correlation characteristics between amino acid residues are extracted by the convolutional operations, and then the long-range interactions between the residues on protein sequences are extracted by the bi-directional long short-term memory network. Finally, the local correlation characteristics and long-range interactions between amino acid residues are employed to predict protein secondary structures. Experimental results show that the proposed model achieves a higher accuracy than the baselines and the framework has good scalability.