Three-Dimensional Graph Matching to Identify Secondary Structure Correspondence of Medium-Resolution Cryo-EM Density Maps

Cryo-electron microscopy (cryo-EM) is a structural technique that has played a significant role in protein structure determination in recent years. Compared to the traditional methods of X-ray crystallography and NMR spectroscopy, cryo-EM is capable of producing images of much larger protein complexes. However, cryo-EM reconstructions are limited to medium-resolution (~4–10 Å) for some cases. At this resolution range, a cryo-EM density map can hardly be used to directly determine the structure of proteins at atomic level resolutions, or even at their amino acid residue backbones. At such a resolution, only the position and orientation of secondary structure elements (SSEs) such as α-helices and β-sheets are observable. Consequently, finding the mapping of the secondary structures of the modeled structure (SSEs-A) to the cryo-EM map (SSEs-C) is one of the primary concerns in cryo-EM modeling. To address this issue, this study proposes a novel automatic computational method to identify SSEs correspondence in three-dimensional (3D) space. Initially, through a modeling of the target sequence with the aid of extracting highly reliable features from a generated 3D model and map, the SSEs matching problem is formulated as a 3D vector matching problem. Afterward, the 3D vector matching problem is transformed into a 3D graph matching problem. Finally, a similarity-based voting algorithm combined with the principle of least conflict (PLC) concept is developed to obtain the SSEs correspondence. To evaluate the accuracy of the method, a testing set of 25 experimental and simulated maps with a maximum of 65 SSEs is selected. Comparative studies are also conducted to demonstrate the superiority of the proposed method over some state-of-the-art techniques. The results demonstrate that the method is efficient, robust, and works well in the presence of errors in the predicted secondary structures of the cryo-EM images

Three-Dimensional Graph Matching to Identify Secondary Structure Correspondence of Medium-Resolution Cryo-EM Density Maps

Cryo-electron microscopy (cryo-EM) is a structural technique that has played a significant role in protein structure determination in recent years. Compared to the traditional methods of X-ray crystallography and NMR spectroscopy, cryo-EM is capable of producing images of much larger protein complexes. However, cryo-EM reconstructions are limited to medium-resolution (~4–10 Å) for some cases. At this resolution range, a cryo-EM density map can hardly be used to directly determine the structure of proteins at atomic level resolutions, or even at their amino acid residue backbones. At such a resolution, only the position and orientation of secondary structure elements (SSEs) such as α-helices and β-sheets are observable. Consequently, finding the mapping of the secondary structures of the modeled structure (SSEs-A) to the cryo-EM map (SSEs-C) is one of the primary concerns in cryo-EM modeling. To address this issue, this study proposes a novel automatic computational method to identify SSEs correspondence in three-dimensional (3D) space. Initially, through a modeling of the target sequence with the aid of extracting highly reliable features from a generated 3D model and map, the SSEs matching problem is formulated as a 3D vector matching problem. Afterward, the 3D vector matching problem is transformed into a 3D graph matching problem. Finally, a similarity-based voting algorithm combined with the principle of least conflict (PLC) concept is developed to obtain the SSEs correspondence. To evaluate the accuracy of the method, a testing set of 25 experimental and simulated maps with a maximum of 65 SSEs is selected. Comparative studies are also conducted to demonstrate the superiority of the proposed method over some state-of-the-art techniques. The results demonstrate that the method is efficient, robust, and works well in the presence of errors in the predicted secondary structures of the cryo-EM images

Online Hybrid Learning Methods for Real-Time Structural Health Monitoring Using Remote Sensing and Small Displacement Data

Structural health monitoring (SHM) by using remote sensing and synthetic aperture radar (SAR) images is a promising approach to assessing the safety and the integrity of civil structures. Apart from this issue, artificial intelligence and machine learning have brought great opportunities to SHM by learning an automated computational model for damage detection. Accordingly, this article proposes online hybrid learning methods to firstly deal with some major challenges in data-driven SHM and secondly detect damage via small displacement data from SAR images in a real-time manner. The proposed methods contain three main parts: (i) data augmentation by Hamiltonian Monte Carlo and slice sampling for addressing the problem of small displacement data, (ii) data normalization by an online deep transfer learning algorithm for removing the effects of environmental and/or operational variability from augmented data, and (iii) feature classification via a scalar novelty score. The major contributions of this research include proposing two online hybrid unsupervised learning methods and providing effective frameworks for online damage detection. A small set of displacement samples extracted from SAR images of TerraSar-X regarding a long-term monitoring scheme of the Tadcaster Bridge in United Kingdom is applied to validate the proposed methods

Elimination of Thermal Effects from Limited Structural Displacements Based on Remote Sensing by Machine Learning Techniques

Confounding variability caused by environmental and/or operational conditions is a big challenge in the structural health monitoring (SHM) of large-scale civil structures. The elimination of such variability is of paramount importance in avoiding economic and human losses. Machine learning-aided data normalization provides a good solution to this challenge. Despite proper studies on data normalization using structural responses/features acquired from contact-based sensors, this issue has not been explored properly via new features, such as displacement responses from remote sensing products, including synthetic aperture radar (SAR) images. Hence, the main aim of this work was to eliminate environmental variability, particularly thermal effects, from different and limited structural displacements retrieved from a few SAR images related to long-term health monitoring programs of long-span bridges. For this purpose, we conducted a comprehensive comparative study to investigate two supervised and two unsupervised data normalization algorithms. The supervised algorithms were based on Gaussian process regression (GPR) and support vector regression (SVR), for which temperature records acquired from contact temperature sensors and structural displacements retrieved from spaceborne remote sensors produce univariate predictor (input) and response (output) data for the regression problem. For the unsupervised algorithms, this paper employed principal component analysis (PCA) and proposed a deep autoencoder (DAE), both of which conform with unsupervised reconstruction-based data normalization. In contrast to the GPR- and SVR-based data normalization algorithms, both the PCA and DAE methods only consider the SAR-based displacement (output) data without any requirement of the environmental and/or operational (input) data. Limited displacement sets of long-span bridges from a few SAR images of Sentinel-1A, related to long-term SHM programs, were considered to assess the aforementioned techniques. Results demonstrate that the proposed DAE-aided data normalization is the best approach to remove thermal effects and other unmeasured environmental and/or operational variability

Detection of Partially Structural Collapse Using Long-Term Small Displacement Data from Satellite Images

The development of satellite sensors and interferometry synthetic aperture radar (InSAR) technology has enabled the exploitation of their benefits for long-term structural health monitoring (SHM). However, some restrictions cause this process to provide a small number of images leading to the problem of small data for SAR-based SHM. Conversely, the major challenge of the long-term monitoring of civil structures pertains to variations in their inherent properties by environmental and/or operational variability. This article aims to propose new hybrid unsupervised learning methods for addressing these challenges. The methods in this work contain three main parts: (i) data augmentation by the Markov Chain Monte Carlo algorithm, (ii) feature normalization, and (iii) decision making via Mahalanobis-squared distance. The first method presented in this work develops an artificial neural network-based feature normalization by proposing an iterative hyperparameter selection of hidden neurons of the network. The second method is a novel unsupervised teacher–student learning by combining an undercomplete deep neural network and an overcomplete single-layer neural network. A small set of long-term displacement samples extracted from a few SAR images of TerraSAR-X is applied to validate the proposed methods. The results show that the methods can effectively deal with the major challenges in the SAR-based SHM applications

{LPTD}: a novel linear programming-based topology determination method for cryo-{EM} maps

Summary: Topology determination is one of the most important intermediate steps towards building the atomic structure of proteins from their medium-resolution cryo-electron microscopy (cryo-EM) map. The main goal in the topology determination is to identify correct matches (i.e. assignment and direction) between secondary structure elements (α-helices and β-sheets) detected in a protein sequence and cryo-EM density map. Despite many recent advances in molecular biology technologies, the problem remains a challenging issue. To overcome the problem, this article proposes a Linear Programming-based Topology Determination method (LPTD) to solve the secondary structure topology problem in three-dimensional geometrical space. Through modeling of the protein's sequence with the aid of extracting highly reliable features and a distance-based scoring function, the secondary structure matching problem is transformed into a complete weighted bipartite graph matching problem. Subsequently, an algorithm based on linear programming is developed as a decision-making strategy to extract the true topology (native topology) between all possible topologies. The proposed automatic framework is verified using 12 experimental and 15 simulated α-β proteins. Results demonstrate that LPTD is highly efficient and extremely fast in such a way that for 77% of cases in the data set, the native topology has been detected in the first rank topology in less than 2 seconds. Besides, this method is able to successfully handle large complex proteins with as many as 65 secondary structure elements. Such a large number of secondary structure elements have never been solved with current tools/methods. Availability: The LPTD package (source code and data) is publicly available at https://github.com/B-Behkamal/LPTD. Moreover, two test samples as well as the instruction of utilizing the graphical user interface (GUI) have been provided in the shared readme file. Supplementary information: Supplementary data will be available at Bioinformatics online