scholarly journals Accurate contact-based modelling of repeat proteins predicts the structure of Curlin and SPW repeats

2019 ◽  
Author(s):  
Claudio Bassot ◽  
Arne Elofsson
Keyword(s):  
Deep Learning ◽  
High Accuracy ◽  
Unique Sequence ◽  
Amino Acid Sequences ◽  
Primary Sequence ◽  
Structure Information ◽  
Repeat Proteins ◽  
Eukaryotic Proteomes ◽  
Direct Coupling Analysis ◽  
Contact Predictions

AbstractRepeat proteins are an abundant class in eukaryotic proteomes. They are involved in many eukaryotic specific functions, including signalling. For many of these families, the structure is not known. Recently, it has been shown that the structure of many protein families can be predicted by using contact predictions from direct coupling analysis and deep learning. However, their unique sequence features present in repeat proteins is a challenge for contact predictions DCA-methods. Here, we show that using the deep learning-based PconsC4 is more effective for predicting both intra and interunit contacts among a comprehensive set of repeat proteins. In a benchmark dataset of 819 repeat proteins about one third can be correctly modelled and among 51 PFAM families lacking a protein structure, we produce models of five families with estimated high accuracy.Author SummaryRepeat proteins are widespread among organisms and particularly abundant in eukaryotic proteomes. Their primary sequence present repetition in the amino acid sequences that origin structures with repeated folds/domains. Although the repeated units are easy to be recognized in primary sequence, often structure information are missing. Here we used contact prediction for predicting the structure of repeats protein directly from their primary sequences. We benchmark our method on a dataset comprehensive of all the known repeated structures. We evaluate the contact predictions and the obtained models set for different classes of proteins and different lengths of the target, and we benchmark the quality assessment of the models on repeats proteins. Finally, we applied the methods on the repeat PFAM families missing of resolved structures, five of them modelled with high accuracy.

scholarly journals Accurate contact-based modelling of repeat proteins predicts the structure of new repeats protein families

2021 ◽  
Vol 17 (4) ◽  
pp. e1008798
Author(s):  
Claudio Bassot ◽  
Arne Elofsson
Keyword(s):  
Deep Learning ◽  
Protein Structure ◽  
High Accuracy ◽  
Unique Sequence ◽  
Direct Coupling ◽  
Protein Families ◽  
Coupling Analysis ◽  
Repeat Proteins ◽  
Eukaryotic Proteomes ◽  
Direct Coupling Analysis

Repeat proteins are abundant in eukaryotic proteomes. They are involved in many eukaryotic specific functions, including signalling. For many of these proteins, the structure is not known, as they are difficult to crystallise. Today, using direct coupling analysis and deep learning it is often possible to predict a protein’s structure. However, the unique sequence features present in repeat proteins have been a challenge to use direct coupling analysis for predicting contacts. Here, we show that deep learning-based methods (trRosetta, DeepMetaPsicov (DMP) and PconsC4) overcomes this problem and can predict intra- and inter-unit contacts in repeat proteins. In a benchmark dataset of 815 repeat proteins, about 90% can be correctly modelled. Further, among 48 PFAM families lacking a protein structure, we produce models of forty-one families with estimated high accuracy.

scholarly journals PconsC4: fast, free, easy, and accurate contact predictions

2018 ◽  
Author(s):  
Mirco Michel ◽  
David Menéndez Hurtado ◽  
Arne Elofsson
Keyword(s):  
Deep Learning ◽  
State Of The Art ◽  
Prediction Methods ◽  
Coupling Analysis ◽  
Learning Methods ◽  
Contact Prediction ◽  
Residue Contact ◽  
Direct Coupling Analysis ◽  
Computationally Expensive ◽  
Contact Predictions

AbstractMotivationResidue contact prediction was revolutionized recently by the introduction of direct coupling analysis (DCA). Further improvements, in particular for small families, have been obtained by the combination of DCA and deep learning methods. However, existing deep learning contact prediction methods often rely on a number of external programs and are therefore computationally expensive.ResultsHere, we introduce a novel contact predictor, PconsC4, which performs on par with state of the art methods. PconsC4 is heavily optimized, does not use any external programs and therefore is significantly faster and easier to use than other methods.AvailabilityPconsC4 is freely available under the GPL license from https://github.com/ElofssonLab/PconsC4. Installation is easy using the pip command and works on any system with Python 3.5 or later and a modern GCC [email protected]

scholarly journals A deep dilated convolutional residual network for predicting interchain contacts of protein homodimers

2021 ◽  
Author(s):  
Raj Shekhor Roy ◽  
Farhan Quadir ◽  
Elham Soltanikazemi ◽  
Jianlin Cheng
Keyword(s):  
Deep Learning ◽  
Tertiary Structure ◽  
Quaternary Structure ◽  
High Accuracy ◽  
Residual Network ◽  
Sequence Alignments ◽  
Learning Methods ◽  
Tertiary Structures ◽  
Residue Contacts ◽  
Contact Predictions

Deep learning has revolutionized protein tertiary structure prediction recently. The cutting-edge deep learning methods such as AlphaFold can predict high-accuracy tertiary structures for most individual protein chains. However, the accuracy of predicting quaternary structures of protein complexes consisting of multiple chains is still relatively low due to lack of advanced deep learning methods in the field. Because interchain residue-residue contacts can be used as distance restraints to guide quaternary structure modeling, here we develop a deep dilated convolutional residual network method (DRCon) to predict interchain residue-residue contacts in homodimers from residue-residue co-evolutionary signals derived from multiple sequence alignments of monomers, intrachain residue-residue contacts of monomers extracted from true/predicted tertiary structures or predicted by deep learning, and other sequence and structural features. Tested on three homodimer test datasets (Homo_std dataset, DeepHomo dataset, and CASP14-CAPRI dataset), the precision of DRCon for top L/5 interchain contact predictions (L: length of monomer in a homodimer) is 43.46%, 47.15%, and 24.81% respectively, which is substantially better than two existing deep learning interchain contact prediction methods. Moreover, our experiments demonstrate that using predicted tertiary structure or intrachain contacts of monomers in the unbound state as input, DRCon still performs reasonably well, even though its accuracy is lower than when true tertiary structures in the bound state are used as input. Finally, our case study shows that good interchain contact predictions can be used to build high-accuracy quaternary structure models of homodimers.

PconsC4: fast, accurate and hassle-free contact predictions

2018 ◽  
Vol 35 (15) ◽  
pp. 2677-2679 ◽  
Author(s):  
Mirco Michel ◽  
David Menéndez Hurtado ◽  
Arne Elofsson
Keyword(s):  
Deep Learning ◽  
State Of The Art ◽  
Supplementary Information ◽  
Prediction Methods ◽  
Coupling Analysis ◽  
Contact Prediction ◽  
Residue Contact ◽  
Direct Coupling Analysis ◽  
Computationally Expensive ◽  
Contact Predictions

Abstract Motivation Residue contact prediction was revolutionized recently by the introduction of direct coupling analysis (DCA). Further improvements, in particular for small families, have been obtained by the combination of DCA and deep learning methods. However, existing deep learning contact prediction methods often rely on a number of external programs and are therefore computationally expensive. Results Here, we introduce a novel contact predictor, PconsC4, which performs on par with state of the art methods. PconsC4 is heavily optimized, does not use any external programs and therefore is significantly faster and easier to use than other methods. Availability and implementation PconsC4 is freely available under the GPL license from https://github.com/ElofssonLab/PconsC4. Installation is easy using the pip command and works on any system with Python 3.5 or later and a GCC compiler. It does not require a GPU nor special hardware. Supplementary information Supplementary data are available at Bioinformatics online.

scholarly journals Augmented Reality Maintenance Assistant Using YOLOv5

2021 ◽  
Vol 11 (11) ◽  
pp. 4758
Author(s):  
Ana Malta ◽  
Mateus Mendes ◽  
Torres Farinha
Keyword(s):  
Neural Network ◽  
Deep Learning ◽  
Object Recognition ◽  
Augmented Reality ◽  
Real Time ◽  
Recognition System ◽  
High Accuracy ◽  
Video Streams ◽  
The Neural Network ◽  
Deep Learning Neural Network

Maintenance professionals and other technical staff regularly need to learn to identify new parts in car engines and other equipment. The present work proposes a model of a task assistant based on a deep learning neural network. A YOLOv5 network is used for recognizing some of the constituent parts of an automobile. A dataset of car engine images was created and eight car parts were marked in the images. Then, the neural network was trained to detect each part. The results show that YOLOv5s is able to successfully detect the parts in real time video streams, with high accuracy, thus being useful as an aid to train professionals learning to deal with new equipment using augmented reality. The architecture of an object recognition system using augmented reality glasses is also designed.

scholarly journals Detecting the pulmonary trunk in CT scout views using deep learning

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Aydin Demircioğlu ◽  
Magdalena Charis Stein ◽  
Moon-Sung Kim ◽  
Henrike Geske ◽  
Anton S. Quinsten ◽  
...  
Keyword(s):  
Deep Learning ◽  
Validation Cohort ◽  
High Accuracy ◽  
Pulmonary Trunk ◽  
Reference Standard ◽  
Bolus Tracking ◽  
Wilcoxon Rank Sum Test ◽  
Scout View ◽  
Axial Ct ◽  
Anterior Posterior

AbstractFor CT pulmonary angiograms, a scout view obtained in anterior–posterior projection is usually used for planning. For bolus tracking the radiographer manually locates a position in the CT scout view where the pulmonary trunk will be visible in an axial CT pre-scan. We automate the task of localizing the pulmonary trunk in CT scout views by deep learning methods. In 620 eligible CT scout views of 563 patients between March 2003 and February 2020 the region of the pulmonary trunk as well as an optimal slice (“reference standard”) for bolus tracking, in which the pulmonary trunk was clearly visible, was annotated and used to train a U-Net predicting the region of the pulmonary trunk in the CT scout view. The networks’ performance was subsequently evaluated on 239 CT scout views from 213 patients and was compared with the annotations of three radiographers. The network was able to localize the region of the pulmonary trunk with high accuracy, yielding an accuracy of 97.5% of localizing a slice in the region of the pulmonary trunk on the validation cohort. On average, the selected position had a distance of 5.3 mm from the reference standard. Compared to radiographers, using a non-inferiority test (one-sided, paired Wilcoxon rank-sum test) the network performed as well as each radiographer (P < 0.001 in all cases). Automated localization of the region of the pulmonary trunk in CT scout views is possible with high accuracy and is non-inferior to three radiographers.

scholarly journals Financial Information Asymmetry: Using Deep Learning Algorithms to Predict Financial Distress

Symmetry ◽  
2021 ◽  
Vol 13 (3) ◽  
pp. 443
Author(s):  
Chyan-long Jan
Keyword(s):  
Neural Networks ◽  
Deep Learning ◽  
Information Asymmetry ◽  
Error Rate ◽  
Financial Distress ◽  
Prediction Models ◽  
High Accuracy ◽  
Financial Information ◽  
Financial Distress Prediction ◽  
Distress Prediction

Because of the financial information asymmetry, the stakeholders usually do not know a company’s real financial condition until financial distress occurs. Financial distress not only influences a company’s operational sustainability and damages the rights and interests of its stakeholders, it may also harm the national economy and society; hence, it is very important to build high-accuracy financial distress prediction models. The purpose of this study is to build high-accuracy and effective financial distress prediction models by two representative deep learning algorithms: Deep neural networks (DNN) and convolutional neural networks (CNN). In addition, important variables are selected by the chi-squared automatic interaction detector (CHAID). In this study, the data of Taiwan’s listed and OTC sample companies are taken from the Taiwan Economic Journal (TEJ) database during the period from 2000 to 2019, including 86 companies in financial distress and 258 not in financial distress, for a total of 344 companies. According to the empirical results, with the important variables selected by CHAID and modeling by CNN, the CHAID-CNN model has the highest financial distress prediction accuracy rate of 94.23%, and the lowest type I error rate and type II error rate, which are 0.96% and 4.81%, respectively.

scholarly journals Deep Learning Based Pavement Inspection Using Self-Reconfigurable Robot

Sensors ◽  
2021 ◽  
Vol 21 (8) ◽  
pp. 2595
Author(s):  
Balakrishnan Ramalingam ◽  
Abdullah Aamir Hayat ◽  
Mohan Rajesh Elara ◽  
Braulio Félix Gómez ◽  
Lim Yi ◽  
...  
Keyword(s):  
Deep Learning ◽  
Semantic Segmentation ◽  
High Accuracy ◽  
Experimental Results ◽  
Mobile Mapping ◽  
Mapping System ◽  
Mobile Mapping System ◽  
Reconfigurable Robot ◽  
Nvidia Gpu ◽  
Inspection Task

The pavement inspection task, which mainly includes crack and garbage detection, is essential and carried out frequently. The human-based or dedicated system approach for inspection can be easily carried out by integrating with the pavement sweeping machines. This work proposes a deep learning-based pavement inspection framework for self-reconfigurable robot named Panthera. Semantic segmentation framework SegNet was adopted to segment the pavement region from other objects. Deep Convolutional Neural Network (DCNN) based object detection is used to detect and localize pavement defects and garbage. Furthermore, Mobile Mapping System (MMS) was adopted for the geotagging of the defects. The proposed system was implemented and tested with the Panthera robot having NVIDIA GPU cards. The experimental results showed that the proposed technique identifies the pavement defects and litters or garbage detection with high accuracy. The experimental results on the crack and garbage detection are presented. It is found that the proposed technique is suitable for deployment in real-time for garbage detection and, eventually, sweeping or cleaning tasks.

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