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PupStruct: Prediction of Pupylated Lysine Residues Using Structural Properties of Amino Acids

Post-translational modification (PTM) is a critical biological reaction which adds to the diversification of the proteome. With numerous known modifications being studied, pupylation has gained focus in the scientific community due to its significant role in regulating biological processes. The trad...

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Detalles Bibliográficos
Autores principales: Singh, Vineet, Sharma, Alok, Dehzangi, Abdollah, Tsunoda, Tatushiko
Formato: Online Artículo Texto
Lenguaje:English
Publicado: MDPI 2020
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7761138/
https://www.ncbi.nlm.nih.gov/pubmed/33260770
http://dx.doi.org/10.3390/genes11121431
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author Singh, Vineet
Sharma, Alok
Dehzangi, Abdollah
Tsunoda, Tatushiko
author_facet Singh, Vineet
Sharma, Alok
Dehzangi, Abdollah
Tsunoda, Tatushiko
author_sort Singh, Vineet
collection PubMed
description Post-translational modification (PTM) is a critical biological reaction which adds to the diversification of the proteome. With numerous known modifications being studied, pupylation has gained focus in the scientific community due to its significant role in regulating biological processes. The traditional experimental practice to detect pupylation sites proved to be expensive and requires a lot of time and resources. Thus, there have been many computational predictors developed to challenge this issue. However, performance is still limited. In this study, we propose another computational method, named PupStruct, which uses the structural information of amino acids with a radial basis kernel function Support Vector Machine (SVM) to predict pupylated lysine residues. We compared PupStruct with three state-of-the-art predictors from the literature where PupStruct has validated a significant improvement in performance over them with statistical metrics such as sensitivity (0.9234), specificity (0.9359), accuracy (0.9296), precision (0.9349), and Mathew’s correlation coefficient (0.8616) on a benchmark dataset.
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spelling pubmed-77611382020-12-26 PupStruct: Prediction of Pupylated Lysine Residues Using Structural Properties of Amino Acids Singh, Vineet Sharma, Alok Dehzangi, Abdollah Tsunoda, Tatushiko Genes (Basel) Article Post-translational modification (PTM) is a critical biological reaction which adds to the diversification of the proteome. With numerous known modifications being studied, pupylation has gained focus in the scientific community due to its significant role in regulating biological processes. The traditional experimental practice to detect pupylation sites proved to be expensive and requires a lot of time and resources. Thus, there have been many computational predictors developed to challenge this issue. However, performance is still limited. In this study, we propose another computational method, named PupStruct, which uses the structural information of amino acids with a radial basis kernel function Support Vector Machine (SVM) to predict pupylated lysine residues. We compared PupStruct with three state-of-the-art predictors from the literature where PupStruct has validated a significant improvement in performance over them with statistical metrics such as sensitivity (0.9234), specificity (0.9359), accuracy (0.9296), precision (0.9349), and Mathew’s correlation coefficient (0.8616) on a benchmark dataset. MDPI 2020-11-28 /pmc/articles/PMC7761138/ /pubmed/33260770 http://dx.doi.org/10.3390/genes11121431 Text en © 2020 by the authors. Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (http://creativecommons.org/licenses/by/4.0/).
spellingShingle Article
Singh, Vineet
Sharma, Alok
Dehzangi, Abdollah
Tsunoda, Tatushiko
PupStruct: Prediction of Pupylated Lysine Residues Using Structural Properties of Amino Acids
title PupStruct: Prediction of Pupylated Lysine Residues Using Structural Properties of Amino Acids
title_full PupStruct: Prediction of Pupylated Lysine Residues Using Structural Properties of Amino Acids
title_fullStr PupStruct: Prediction of Pupylated Lysine Residues Using Structural Properties of Amino Acids
title_full_unstemmed PupStruct: Prediction of Pupylated Lysine Residues Using Structural Properties of Amino Acids
title_short PupStruct: Prediction of Pupylated Lysine Residues Using Structural Properties of Amino Acids
title_sort pupstruct: prediction of pupylated lysine residues using structural properties of amino acids
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7761138/
https://www.ncbi.nlm.nih.gov/pubmed/33260770
http://dx.doi.org/10.3390/genes11121431
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