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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| Format: | Article |
| Language: | English |
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MDPI AG
2020-11-01
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| Series: | Genes |
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| Online Access: | https://www.mdpi.com/2073-4425/11/12/1431 |
| _version_ | 1797546362223460352 |
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| author | Vineet Singh Alok Sharma Abdollah Dehzangi Tatushiko Tsunoda |
| author_facet | Vineet Singh Alok Sharma Abdollah Dehzangi Tatushiko Tsunoda |
| author_sort | Vineet Singh |
| collection | DOAJ |
| 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. |
| first_indexed | 2024-03-10T14:28:50Z |
| format | Article |
| id | doaj.art-1452c8d139e44e9caa08ad859ed63742 |
| institution | Directory Open Access Journal |
| issn | 2073-4425 |
| language | English |
| last_indexed | 2024-03-10T14:28:50Z |
| publishDate | 2020-11-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Genes |
| spelling | doaj.art-1452c8d139e44e9caa08ad859ed637422023-11-20T22:43:17ZengMDPI AGGenes2073-44252020-11-011112143110.3390/genes11121431PupStruct: Prediction of Pupylated Lysine Residues Using Structural Properties of Amino AcidsVineet Singh0Alok Sharma1Abdollah Dehzangi2Tatushiko Tsunoda3Faculty of Science Technology and Environment, University of the South Pacific, Suva, FijiInstitute for Integrated and Intelligent Systems, Griffith University, Brisbane, QLD 4111, AustraliaDepartment of Computer Science, Rutgers University, Camden, NJ 08102, USALaboratory for Medical Science Mathematics, RIKEN Center for Integrative Medical Sciences, Yokohama 230-0045, JapanPost-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.https://www.mdpi.com/2073-4425/11/12/1431post-translational modification (PTM)lysine pupylationstructural featuresprotein sequencesamino acidsprediction |
| spellingShingle | Vineet Singh Alok Sharma Abdollah Dehzangi Tatushiko Tsunoda PupStruct: Prediction of Pupylated Lysine Residues Using Structural Properties of Amino Acids Genes post-translational modification (PTM) lysine pupylation structural features protein sequences amino acids prediction |
| 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 | post-translational modification (PTM) lysine pupylation structural features protein sequences amino acids prediction |
| url | https://www.mdpi.com/2073-4425/11/12/1431 |
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