Deep Convolutional Neural Networks for Detecting Secondary Structures in Protein Density Maps from Cryo-Electron Microscopy

Proceedings
Rongjian LiJing He

Abstract

The detection of secondary structure of proteins using three dimensional (3D) cryo-electron microscopy (cryo-EM) images is still a challenging task when the spatial resolution of cryo-EM images is at medium level (5-10Å ). Prior researches focused on the usage of local features that may not capture the global information of image objects. In this study, we propose to use deep learning methods to extract high representative global features and then automatically detect secondary structures of proteins. In particular, we build a convolutional neural network (CNN) classifier that predicts the probability of label for every individual voxel in 3D cryo-EM image with respect to the secondary structure elements of proteins such as α-helix, β-sheet and background. To effectively incorporate the 3D spatial information in protein structures, we propose to perform 3D convolutions in the convolutional layers of CNNs. We show that the proposed CNN classifier can outperform existing SVM method on identifying the secondary structure elements of proteins from 3D cryo-EM medium resolution images.

Citations

Dec 28, 2019·Molecules : a Journal of Synthetic Chemistry and Natural Product Chemistry·Eman Alnabati, Daisuke Kihara
Jul 31, 2019·Nature Methods·Sai Raghavendra Maddhuri Venkata SubramaniyaDaisuke Kihara
Oct 17, 2017·Journal of Computational Biology : a Journal of Computational Molecular Cell Biology·Albert Ng, Dong Si
Nov 30, 2018·Histochemistry and Cell Biology·K Shaga DevanC Read
Jan 1, 2021·The Journal of Chemical Physics·Justin T Seffernick, Steffen Lindert

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