iProtGly‐SS: Identifying protein glycation sites using sequence and structure based features

Glycation is chemical reaction by which sugar molecule bonds with a protein without the help of enzymes. This is often cause to many diseases and therefore the knowledge about glycation is very important. In this paper, we present iProtGly‐SS, a protein lysine glycation site identification method ba...

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Veröffentlicht in:Proteins, structure, function, and bioinformatics structure, function, and bioinformatics, 2018-07, Vol.86 (7), p.777-789
Hauptverfasser: Islam, Md Mofijul, Saha, Sanjay, Rahman, Md Mahmudur, Shatabda, Swakkhar, Farid, Dewan Md, Dehzangi, Abdollah
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container_end_page 789
container_issue 7
container_start_page 777
container_title Proteins, structure, function, and bioinformatics
container_volume 86
creator Islam, Md Mofijul
Saha, Sanjay
Rahman, Md Mahmudur
Shatabda, Swakkhar
Farid, Dewan Md
Dehzangi, Abdollah
description Glycation is chemical reaction by which sugar molecule bonds with a protein without the help of enzymes. This is often cause to many diseases and therefore the knowledge about glycation is very important. In this paper, we present iProtGly‐SS, a protein lysine glycation site identification method based on features extracted from sequence and secondary structural information. In the experiments, we found the best feature groups combination: Amino Acid Composition, Secondary Structure Motifs, and Polarity. We used support vector machine classifier to train our model and used an optimal set of features using a group based forward feature selection technique. On standard benchmark datasets, our method is able to significantly outperform existing methods for glycation prediction. A web server for iProtGly‐SS is implemented and publicly available to use: http://brl.uiu.ac.bd/iprotgly-ss/.
doi_str_mv 10.1002/prot.25511
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subjects Amino acid composition
Amino acid sequence
Chemical bonds
Chemical reactions
classification
evolutionary features
Feature extraction
feature selection
Glycosylation
Internet
Lysine
Molecular chains
Organic chemistry
Polarity
protein glycation
Protein structure
Proteins
Secondary structure
Servers
structural features
Sugar
Support vector machines
title iProtGly‐SS: Identifying protein glycation sites using sequence and structure based features
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