论文标题
PS8-NET:深卷卷神经网络,以预测八态蛋白二级结构
PS8-Net: A Deep Convolutional Neural Network to Predict the Eight-State Protein Secondary Structure
论文作者
论文摘要
蛋白质二级结构对于在主要和第三(3D)结构之间建立信息桥至关重要。八状态蛋白二级结构(PSS)的精确预测已在生物信息学中的蛋白质结构和功能分析中显着使用。最近在该研究领域应用了深度学习技术,并提高了八态(Q8)蛋白二级结构预测的准确性。然而,从理论的角度来看,仍然有很多改进的房间,特别是在八态PSS预测中。在这项研究中,我们提出了一个新的深卷积神经网络(DCNN),即PS8-NET,以提高八类PSS预测的准确性。该体系结构的输入是来自蛋白质序列特征和配置功能的精心构造的特征矩阵。我们在网络中引入了一个新的PS8模块,该模块与SKIP连接一起应用,以从较高层中提取长期相互依赖性,从而在较早的层中获取局部环境,并在二级结构预测期间实现全局信息。我们提出的PS8-NET在基准CULLPDB6133,CB513,CASP10和CASP11数据集上分别达到76.89%,71.94%,76.86%和75.26%的Q8精度。该体系结构可以有效地处理氨基酸之间的局部和全局相互依赖性,以对每个类别进行准确的预测。据我们所知,PS8-NET实验结果表明,它的表现优于上述基准数据集上的所有最新方法。
Protein secondary structure is crucial to creating an information bridge between the primary and tertiary (3D) structures. Precise prediction of eight-state protein secondary structure (PSS) has significantly utilized in the structural and functional analysis of proteins in bioinformatics. Deep learning techniques have been recently applied in this research area and raised the eight-state (Q8) protein secondary structure prediction accuracy remarkably. Nevertheless, from a theoretical standpoint, there are still lots of rooms for improvement, specifically in the eight-state PSS prediction. In this study, we have presented a new deep convolutional neural network (DCNN), namely PS8-Net, to enhance the accuracy of eight-class PSS prediction. The input of this architecture is a carefully constructed feature matrix from the proteins sequence features and profile features. We introduce a new PS8 module in the network, which is applied with skip connection to extracting the long-term inter-dependencies from higher layers, obtaining local contexts in earlier layers, and achieving global information during secondary structure prediction. Our proposed PS8-Net achieves 76.89%, 71.94%, 76.86%, and 75.26% Q8 accuracy respectively on benchmark CullPdb6133, CB513, CASP10, and CASP11 datasets. This architecture enables the efficient processing of local and global interdependencies between amino acids to make an accurate prediction of each class. To the best of our knowledge, PS8-Net experiment results demonstrate that it outperforms all the state-of-the-art methods on the aforementioned benchmark datasets.