scholarly journals Deep Learning to Predict Protein Backbone Structure from High-Resolution Cryo-EM Density Maps

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Dong Si ◽  
Spencer A. Moritz ◽  
Jonas Pfab ◽  
Jie Hou ◽  
Renzhi Cao ◽  
...  
2019 ◽  
Author(s):  
Spencer A. Moritz ◽  
Jonas Pfab ◽  
Tianqi Wu ◽  
Jie Hou ◽  
Jianlin Cheng ◽  
...  

AbstractCryo-electron microscopy (cryo-EM) has become a leading technology for determining protein structures. Recent advances in this field have allowed for atomic resolution. However, predicting the backbone trace of a protein has remained a challenge on all but the most pristine density maps (< 2.5Å resolution). Here we introduce a deep learning model that uses a set of cascaded convolutional neural networks (CNNs) to predict Cα atoms along a protein’s backbone structure. The cascaded-CNN (C-CNN) is a novel deep learning architecture comprised of multiple CNNs, each predicting a specific aspect of a protein’s structure. This model predicts secondary structure elements (SSEs), backbone structure, and Cα atoms, combining the results of each to produce a complete prediction map. The cascaded-CNN is a semantic segmentation image classifier and was trained using thousands of simulated density maps. This method is largely automatic and only requires a recommended threshold value for each evaluated protein. A specialized tabu-search path walking algorithm was used to produce an initial backbone trace with Cα placements. A helix-refinement algorithm made further improvements to the α-helix SSEs of the backbone trace. Finally, a novel quality assessment-based combinatorial algorithm was used to effectively map Cα traces to obtain full-atom protein structures. This method was tested on 50 experimental maps between 2.6Å and 4.4Å resolution. It outperformed several state-of-the-art prediction methods including RosettaES, MAINMAST, and a Phenix based method by producing the most complete prediction models, as measured by percentage of found Cα atoms. This method accurately predicted 88.5% (mean) of the Cα atoms within 3Å of a protein’s backbone structure surpassing the 66.8% mark achieved by the leading alternate method (Phenix based fully automatic method) on the same set of density maps. The C-CNN also achieved an average RMSD of 1.23Å for all 50 experimental density maps which is similar to the Phenix based fully automatic method. The source code and demo of this research has been published athttps://github.com/DrDongSi/Ca-Backbone-Prediction.


Author(s):  
H.A. Cohen ◽  
T.W. Jeng ◽  
W. Chiu

This tutorial will discuss the methodology of low dose electron diffraction and imaging of crystalline biological objects, the problems of data interpretation for two-dimensional projected density maps of glucose embedded protein crystals, the factors to be considered in combining tilt data from three-dimensional crystals, and finally, the prospects of achieving a high resolution three-dimensional density map of a biological crystal. This methodology will be illustrated using two proteins under investigation in our laboratory, the T4 DNA helix destabilizing protein gp32*I and the crotoxin complex crystal.


2021 ◽  
Vol 13 (12) ◽  
pp. 2326
Author(s):  
Xiaoyong Li ◽  
Xueru Bai ◽  
Feng Zhou

A deep-learning architecture, dubbed as the 2D-ADMM-Net (2D-ADN), is proposed in this article. It provides effective high-resolution 2D inverse synthetic aperture radar (ISAR) imaging under scenarios of low SNRs and incomplete data, by combining model-based sparse reconstruction and data-driven deep learning. Firstly, mapping from ISAR images to their corresponding echoes in the wavenumber domain is derived. Then, a 2D alternating direction method of multipliers (ADMM) is unrolled and generalized to a deep network, where all adjustable parameters in the reconstruction layers, nonlinear transform layers, and multiplier update layers are learned by an end-to-end training through back-propagation. Since the optimal parameters of each layer are learned separately, 2D-ADN exhibits more representation flexibility and preferable reconstruction performance than model-driven methods. Simultaneously, it is able to better facilitate ISAR imaging with limited training samples than data-driven methods owing to its simple structure and small number of adjustable parameters. Additionally, benefiting from the good performance of 2D-ADN, a random phase error estimation method is proposed, through which well-focused imaging can be acquired. It is demonstrated by experiments that although trained by only a few simulated images, the 2D-ADN shows good adaptability to measured data and favorable imaging results with a clear background can be obtained in a short time.


Drones ◽  
2021 ◽  
Vol 5 (1) ◽  
pp. 6
Author(s):  
Apostolos Papakonstantinou ◽  
Marios Batsaris ◽  
Spyros Spondylidis ◽  
Konstantinos Topouzelis

Marine litter (ML) accumulation in the coastal zone has been recognized as a major problem in our time, as it can dramatically affect the environment, marine ecosystems, and coastal communities. Existing monitoring methods fail to respond to the spatiotemporal changes and dynamics of ML concentrations. Recent works showed that unmanned aerial systems (UAS), along with computer vision methods, provide a feasible alternative for ML monitoring. In this context, we proposed a citizen science UAS data acquisition and annotation protocol combined with deep learning techniques for the automatic detection and mapping of ML concentrations in the coastal zone. Five convolutional neural networks (CNNs) were trained to classify UAS image tiles into two classes: (a) litter and (b) no litter. Testing the CCNs’ generalization ability to an unseen dataset, we found that the VVG19 CNN returned an overall accuracy of 77.6% and an f-score of 77.42%. ML density maps were created using the automated classification results. They were compared with those produced by a manual screening classification proving our approach’s geographical transferability to new and unknown beaches. Although ML recognition is still a challenging task, this study provides evidence about the feasibility of using a citizen science UAS-based monitoring method in combination with deep learning techniques for the quantification of the ML load in the coastal zone using density maps.


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