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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...
Autores principales: | , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
MDPI
2020
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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. |
format | Online Article Text |
id | pubmed-7761138 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2020 |
publisher | MDPI |
record_format | MEDLINE/PubMed |
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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