scholarly journals A single-model quality assessment method for poor quality protein structure

2020 ◽  
Author(s):  
Jianquan Ouyang ◽  
Ningqiao Huang ◽  
Yunqi Jiang
Keyword(s):  
Protein Structure ◽  
Quality Assessment ◽  
Structure Prediction ◽  
Assessment Method ◽  
Poor Quality ◽  
Single Model ◽  
Model Quality ◽  
Model Quality Assessment ◽  
Quality Assessment Method

Abstract Background: Quality assessment of protein tertiary structure prediction models, in which structures of the best quality are selected from decoys, is a major challenge in protein structure prediction, and is crucial to determine a model’s utility and potential applications. Estimating the quality of a single model predicts the model’s quality based on the single model itself. In general, the Pearson correlation value of the quality assessment method increases in tandem with an increase in the quality of the model pool. However, there is no consensus regarding the best method to select a few good models from the poor quality model pool.Results: We introduce a novel single-model quality assessment method for poor quality models that uses simple linear combinations of six features. We perform weighted search and linear regression on a large dataset of models from the 12th Critical Assessment of Protein Structure Prediction (CASP12) and benchmark the results on CASP13 models. We demonstrate that our method achieves outstanding performance on poor quality models.Conclusions: According to results of poor protein structure assessment based on six features, contact prediction and relying on fewer prediction features can improve selection accuracy.

scholarly journals A single-model quality assessment method for poor quality protein structure

2020 ◽  
Author(s):  
Jianquan Ouyang ◽  
Ningqiao Huang ◽  
Yunqi Jiang
Keyword(s):  
Protein Structure ◽  
Quality Assessment ◽  
Structure Prediction ◽  
Assessment Method ◽  
Poor Quality ◽  
Single Model ◽  
Model Quality ◽  
Model Quality Assessment ◽  
Quality Assessment Method

Abstract Quality assessment of protein tertiary structure prediction models, in which structures of the best quality are selected from decoys, is a major challenge in protein structure prediction, and is crucial to determine a model’s utility and potential applications. Estimating the quality of a single model predicts the model’s quality based on the single model itself. In general, the Pearson correlation value of the quality assessment method increases in tandem with an increase in the quality of the model pool. However, there is no consensus regarding the best method to select a few good models from the poor quality model pool. In this work, we introduce a novel single-model quality assessment method for poor quality models that uses simple linear combinations of six features. We perform weighted search and linear regression on a large dataset of models from the 12th Critical Assessment of Protein Structure Prediction (CASP12) and benchmark the results on CASP13 models. We demonstrate that our method achieves outstanding performance on poor quality models.

scholarly journals Model Quality Assessment Method Based on Support Vector Machine

2021 ◽  
Vol 25 (1) ◽  
pp. 35-39
Author(s):  
Łukasz Glodek ◽  
Szymon Bysko ◽  
Witold Nocoń
Keyword(s):  
Support Vector Machine ◽  
Quality Assessment ◽  
Industry 4.0 ◽  
Assessment Method ◽  
Support Vector ◽  
Model Quality ◽  
Digital Twin ◽  
Model Quality Assessment ◽  
Virtual Commissioning ◽  
Quality Assessment Method

This paper proposes a model quality assessment method based on Support Vector Machine, which can be used to develop a digital twin. This work is strongly connected with Industry 4.0, in which the main idea is to integrate machines, devices, systems, and IT. One of the goals of Industry 4.0 is to introduce flexible assortment changes. Virtual commissioning can be used to create a simulation model of a plant or conduct training for maintenance engineers. On a branch of virtual commissioning is a digital twin. The digital twin is a virtual representation of a plant or a device. Thanks to the digital twin, different scenarios can be analyzed to make the testing process less complicated and less time-consuming. The goal of this work is to propose a coefficient that will take into account expert knowledge and methods used for model quality assessment (such as Normalized Root Mean Square Error – NRMSE, Maximum Error – ME). NRMSE and ME methods are commonly used for this purpose, but they have not been used simultaneously so far. Each of them takes into consideration another aspect of a model. The coefficient allows deciding whether the model can be used for digital twin appliances. Such an attitude introduces the ability to test models automatically or in a semi-automatic way.

scholarly journals P3CMQA: Single-Model Quality Assessment Using 3DCNN with Profile-Based Features

2021 ◽  
Vol 8 (3) ◽  
pp. 40
Author(s):  
Yuma Takei ◽  
Takashi Ishida
Keyword(s):  
Quality Assessment ◽  
Structure Prediction ◽  
Tertiary Structure ◽  
Protein Structures ◽  
Three Dimensional ◽  
Sequence Profile ◽  
Single Model ◽  
Model Quality ◽  
Model Quality Assessment ◽  
Assessment Performance

Model quality assessment (MQA), which selects near-native structures from structure models, is an important process in protein tertiary structure prediction. The three-dimensional convolution neural network (3DCNN) was applied to the task, but the performance was comparable to existing methods because it used only atom-type features as the input. Thus, we added sequence profile-based features, which are also used in other methods, to improve the performance. We developed a single-model MQA method for protein structures based on 3DCNN using sequence profile-based features, namely, P3CMQA. Performance evaluation using a CASP13 dataset showed that profile-based features improved the assessment performance, and the proposed method was better than currently available single-model MQA methods, including the previous 3DCNN-based method. We also implemented a web-interface of the method to make it more user-friendly.

scholarly journals De novo protein structure prediction by incremental inter-residue geometries prediction and model quality assessment using deep learning

2022 ◽  
Author(s):  
Jun Liu ◽  
Guangxing He ◽  
Kailong Zhao ◽  
Guijun Zhang
Keyword(s):  
Protein Structure ◽  
Quality Assessment ◽  
Protein Structure Prediction ◽  
Structure Prediction ◽  
De Novo ◽  
Feedback Mechanism ◽  
Geometric Constraints ◽  
Model Quality ◽  
Model Quality Assessment ◽  
Loop Feedback

Motivation: The successful application of deep learning has promoted progress in protein model quality assessment. How to use model quality assessment to further improve the accuracy of protein structure prediction, especially not reliant on the existing templates, is helpful for unraveling the folding mechanism. Here, we investigate whether model quality assessment can be introduced into structure prediction to form a closed-loop feedback, and iteratively improve the accuracy of de novo protein structure prediction. Results: In this study, we propose a de novo protein structure prediction method called RocketX. In RocketX, a feedback mechanism is constructed through the geometric constraint prediction network GeomNet, the structural simulation module, and the model quality evaluation network EmaNet. In GeomNet, the co-evolutionary features extracted from MSA that search from the sequence databases are sent to an improved residual neural network to predict the inter-residue geometric constraints. The structure model is folded based on the predicted geometric constraints. In EmaNet, the 1D and 2D features are extracted from the folded model and sent to the deep residual neural network to estimate the inter-residue distance deviation and per-residue lDDT of the model, which will be fed back to GeomNet as dynamic features to correct the geometries prediction and progressively improve model accuracy. RocketX is tested on 483 benchmark proteins and 20 FM targets of CASP14. Experimental results show that the closed-loop feedback mechanism significantly contributes to the performance of RocketX, and the prediction accuracy of RocketX outperforms that of the state-of-the-art methods trRosetta (without templates) and RaptorX. In addition, the blind test results on CAMEO show that although no template is used, the prediction accuracy of RocketX on medium and hard targets is comparable to the advanced methods that integrate templates.

scholarly journals A multilayer evaluation approach for protein structure prediction and model quality assessment

2011 ◽  
Vol 79 (S10) ◽  
pp. 172-184 ◽  
Author(s):  
Jingfen Zhang ◽  
Qingguo Wang ◽  
Kittinun Vantasin ◽  
Jiong Zhang ◽  
Zhiquan He ◽  
...  
Keyword(s):  
Protein Structure ◽  
Quality Assessment ◽  
Protein Structure Prediction ◽  
Structure Prediction ◽  
Model Quality ◽  
Model Quality Assessment ◽  
Evaluation Approach

scholarly journals AngularQA: Protein Model Quality Assessment with LSTM Networks

2019 ◽  
Vol 7 (1) ◽  
pp. 1-9 ◽  
Author(s):  
Matthew Conover ◽  
Max Staples ◽  
Dong Si ◽  
Miao Sun ◽  
Renzhi Cao
Keyword(s):  
Protein Structure ◽  
Quality Assessment ◽  
Protein Structure Prediction ◽  
Structure Prediction ◽  
Poor Quality ◽  
Model Quality ◽  
Time Step ◽  
Testing Dataset ◽  
Protein Model Quality Assessment ◽  
Lstm Network

AbstractQuality Assessment (QA) plays an important role in protein structure prediction. Traditional multimodel QA method usually suffer from searching databases or comparing with other models for making predictions, which usually fail when the poor quality models dominate the model pool. We propose a novel protein single-model QA method which is built on a new representation that converts raw atom information into a series of carbon-alpha (Cα) atoms with side-chain information, defined by their dihedral angles and bond lengths to the prior residue. An LSTM network is used to predict the quality by treating each amino acid as a time-step and consider the final value returned by the LSTM cells. To the best of our knowledge, this is the first time anyone has attempted to use an LSTM model on the QA problem; furthermore, we use a new representation which has not been studied for QA. In addition to angles, we make use of sequence properties like secondary structure parsed from protein structure at each time-step without using any database, which is different than all existed QA methods. Our model achieves an overall correlation of 0.651 on the CASP12 testing dataset. Our experiment points out new directions for QA problem and our method could be widely used for protein structure prediction problem. The software is freely available at GitHub: https://github.com/caorenzhi/AngularQA

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