GlyStruct: glycation prediction using structural properties of amino acid residues
Abstract Background Glycation is a one of the post-translational modifications (PTM) where sugar molecules and residues in protein sequences are covalently bonded. It has become one of the clinically important PTM in recent times attributed to many chronic and age related complications. Being a non-...
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doaj-3c97e4ab186f410bb5628ba7c3bdbf002020-11-25T01:15:07ZengBMCBMC Bioinformatics1471-21052019-02-0119S13556410.1186/s12859-018-2547-xGlyStruct: glycation prediction using structural properties of amino acid residuesHamendra Manhar Reddy0Alok Sharma1Abdollah Dehzangi2Daichi Shigemizu3Abel Avitesh Chandra4Tatushiko Tsunoda5School of Engineering & Physics, University of the South PacificSchool of Engineering & Physics, University of the South PacificDepartment of Computer Science, Morgan State UniversityLaboratory for Medical Science Mathematics, RIKEN Center for Integrative Medical SciencesSchool of Engineering & Physics, University of the South PacificLaboratory for Medical Science Mathematics, RIKEN Center for Integrative Medical SciencesAbstract Background Glycation is a one of the post-translational modifications (PTM) where sugar molecules and residues in protein sequences are covalently bonded. It has become one of the clinically important PTM in recent times attributed to many chronic and age related complications. Being a non-enzymatic reaction, it is a great challenge when it comes to its prediction due to the lack of significant bias in the sequence motifs. Results We developed a classifier, GlyStruct based on support vector machine, to predict glycated and non-glycated lysine residues using structural properties of amino acid residues. The features used were secondary structure, accessible surface area and the local backbone torsion angles. For this work, a benchmark dataset was extracted containing 235 glycated and 303 non-glycated lysine residues. GlyStruct demonstrated improved performance of approximately 10% in comparison to benchmark method of Gly-PseAAC. The performance for GlyStruct on the metrics, sensitivity, specificity, accuracy and Mathew’s correlation coefficient were 0.7013, 0.7989, 0.7562, and 0.5065, respectively for 10-fold cross-validation. Conclusion Glycation has emerged to be one of the clinically important PTM of proteins in recent times. Therefore, the development of computational tools become necessary to predict glycation, which could help medical professionals administer drugs and manage patients more effectively. The proposed predictor manages to classify glycated and non-glycated lysine residues with promising results consistently on various cross-validation schemes and outperforms other state of the art methods.http://link.springer.com/article/10.1186/s12859-018-2547-xPost-translational modificationLysine glycationProtein sequencesAmino acidsPredictionSupport vector machine |
collection |
DOAJ |
language |
English |
format |
Article |
sources |
DOAJ |
author |
Hamendra Manhar Reddy Alok Sharma Abdollah Dehzangi Daichi Shigemizu Abel Avitesh Chandra Tatushiko Tsunoda |
spellingShingle |
Hamendra Manhar Reddy Alok Sharma Abdollah Dehzangi Daichi Shigemizu Abel Avitesh Chandra Tatushiko Tsunoda GlyStruct: glycation prediction using structural properties of amino acid residues BMC Bioinformatics Post-translational modification Lysine glycation Protein sequences Amino acids Prediction Support vector machine |
author_facet |
Hamendra Manhar Reddy Alok Sharma Abdollah Dehzangi Daichi Shigemizu Abel Avitesh Chandra Tatushiko Tsunoda |
author_sort |
Hamendra Manhar Reddy |
title |
GlyStruct: glycation prediction using structural properties of amino acid residues |
title_short |
GlyStruct: glycation prediction using structural properties of amino acid residues |
title_full |
GlyStruct: glycation prediction using structural properties of amino acid residues |
title_fullStr |
GlyStruct: glycation prediction using structural properties of amino acid residues |
title_full_unstemmed |
GlyStruct: glycation prediction using structural properties of amino acid residues |
title_sort |
glystruct: glycation prediction using structural properties of amino acid residues |
publisher |
BMC |
series |
BMC Bioinformatics |
issn |
1471-2105 |
publishDate |
2019-02-01 |
description |
Abstract Background Glycation is a one of the post-translational modifications (PTM) where sugar molecules and residues in protein sequences are covalently bonded. It has become one of the clinically important PTM in recent times attributed to many chronic and age related complications. Being a non-enzymatic reaction, it is a great challenge when it comes to its prediction due to the lack of significant bias in the sequence motifs. Results We developed a classifier, GlyStruct based on support vector machine, to predict glycated and non-glycated lysine residues using structural properties of amino acid residues. The features used were secondary structure, accessible surface area and the local backbone torsion angles. For this work, a benchmark dataset was extracted containing 235 glycated and 303 non-glycated lysine residues. GlyStruct demonstrated improved performance of approximately 10% in comparison to benchmark method of Gly-PseAAC. The performance for GlyStruct on the metrics, sensitivity, specificity, accuracy and Mathew’s correlation coefficient were 0.7013, 0.7989, 0.7562, and 0.5065, respectively for 10-fold cross-validation. Conclusion Glycation has emerged to be one of the clinically important PTM of proteins in recent times. Therefore, the development of computational tools become necessary to predict glycation, which could help medical professionals administer drugs and manage patients more effectively. The proposed predictor manages to classify glycated and non-glycated lysine residues with promising results consistently on various cross-validation schemes and outperforms other state of the art methods. |
topic |
Post-translational modification Lysine glycation Protein sequences Amino acids Prediction Support vector machine |
url |
http://link.springer.com/article/10.1186/s12859-018-2547-x |
work_keys_str_mv |
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