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Accurate Identification of Antioxidant Proteins Based on a Combination of Machine Learning Techniques and Hidden Markov Model Profiles

Antioxidant proteins (AOPs) play important roles in the management and prevention of several human diseases due to their ability to neutralize excess free radicals. However, the identification of AOPs by using wet-lab experimental techniques is often time-consuming and expensive. In this study, we p...

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Detalles Bibliográficos
Autores principales: Shen, Zhehan, Liu, Taigang, Xu, Ting
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Hindawi 2021
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8369162/
https://www.ncbi.nlm.nih.gov/pubmed/34413898
http://dx.doi.org/10.1155/2021/5770981
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author Shen, Zhehan
Liu, Taigang
Xu, Ting
author_facet Shen, Zhehan
Liu, Taigang
Xu, Ting
author_sort Shen, Zhehan
collection PubMed
description Antioxidant proteins (AOPs) play important roles in the management and prevention of several human diseases due to their ability to neutralize excess free radicals. However, the identification of AOPs by using wet-lab experimental techniques is often time-consuming and expensive. In this study, we proposed an accurate computational model, called AOP-HMM, to predict AOPs by extracting discriminatory evolutionary features from hidden Markov model (HMM) profiles. First, auto cross-covariance (ACC) variables were applied to transform the HMM profiles into fixed-length feature vectors. Then, we performed the analysis of variance (ANOVA) method to reduce the dimensionality of the raw feature space. Finally, a support vector machine (SVM) classifier was adopted to conduct the prediction of AOPs. To comprehensively evaluate the performance of the proposed AOP-HMM model, the 10-fold cross-validation (CV), the jackknife CV, and the independent test were carried out on two widely used benchmark datasets. The experimental results demonstrated that AOP-HMM outperformed most of the existing methods and could be used to quickly annotate AOPs and guide the experimental process.
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spelling pubmed-83691622021-08-18 Accurate Identification of Antioxidant Proteins Based on a Combination of Machine Learning Techniques and Hidden Markov Model Profiles Shen, Zhehan Liu, Taigang Xu, Ting Comput Math Methods Med Research Article Antioxidant proteins (AOPs) play important roles in the management and prevention of several human diseases due to their ability to neutralize excess free radicals. However, the identification of AOPs by using wet-lab experimental techniques is often time-consuming and expensive. In this study, we proposed an accurate computational model, called AOP-HMM, to predict AOPs by extracting discriminatory evolutionary features from hidden Markov model (HMM) profiles. First, auto cross-covariance (ACC) variables were applied to transform the HMM profiles into fixed-length feature vectors. Then, we performed the analysis of variance (ANOVA) method to reduce the dimensionality of the raw feature space. Finally, a support vector machine (SVM) classifier was adopted to conduct the prediction of AOPs. To comprehensively evaluate the performance of the proposed AOP-HMM model, the 10-fold cross-validation (CV), the jackknife CV, and the independent test were carried out on two widely used benchmark datasets. The experimental results demonstrated that AOP-HMM outperformed most of the existing methods and could be used to quickly annotate AOPs and guide the experimental process. Hindawi 2021-08-07 /pmc/articles/PMC8369162/ /pubmed/34413898 http://dx.doi.org/10.1155/2021/5770981 Text en Copyright © 2021 Zhehan Shen et al. https://creativecommons.org/licenses/by/4.0/This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Research Article
Shen, Zhehan
Liu, Taigang
Xu, Ting
Accurate Identification of Antioxidant Proteins Based on a Combination of Machine Learning Techniques and Hidden Markov Model Profiles
title Accurate Identification of Antioxidant Proteins Based on a Combination of Machine Learning Techniques and Hidden Markov Model Profiles
title_full Accurate Identification of Antioxidant Proteins Based on a Combination of Machine Learning Techniques and Hidden Markov Model Profiles
title_fullStr Accurate Identification of Antioxidant Proteins Based on a Combination of Machine Learning Techniques and Hidden Markov Model Profiles
title_full_unstemmed Accurate Identification of Antioxidant Proteins Based on a Combination of Machine Learning Techniques and Hidden Markov Model Profiles
title_short Accurate Identification of Antioxidant Proteins Based on a Combination of Machine Learning Techniques and Hidden Markov Model Profiles
title_sort accurate identification of antioxidant proteins based on a combination of machine learning techniques and hidden markov model profiles
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8369162/
https://www.ncbi.nlm.nih.gov/pubmed/34413898
http://dx.doi.org/10.1155/2021/5770981
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