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primary topic: NAGbinder: An approach for identifying N-acetylglucosamine interacting residues of a protein from its primary sequence.

NAGbinder: An approach for identifying N-acetylglucosamine interacting residues of a protein from its primary sequence.
type: AcademicArticle
type: Article
abstract: N-acetylglucosamine (NAG) belongs to the eight essential saccharides that are required to maintain the optimal health and precise functioning of systems ranging from bacteria to human. In the present study, we have developed a method, NAGbinder, which predicts the NAG-interacting residues in a protein from its primary sequence information. We extracted 231 NAG-interacting nonredundant protein chains from Protein Data Bank, where no two sequences share more than 40% sequence identity. All prediction models were trained, validated, and evaluated on these 231 protein chains. At first, prediction models were developed on balanced data consisting of 1,335 NAG-interacting and noninteracting residues, using various window size. The model developed by implementing Random Forest using binary profiles as the main principle for identifying NAG-interacting residue with window size 9, performed best among other models. It achieved highest Matthews Correlation Coefficient (MCC) of 0.31 and 0.25, and Area Under Receiver Operating Curve (AUROC) of 0.73 and 0.70 on training and validation data set, respectively. We also developed prediction models on realistic data set (1,335 NAG-interacting and 47,198 noninteracting residues) using the same principle, where the model achieved MCC of 0.26 and 0.27, and AUROC of 0.70 and 0.71, on training and validation data set, respectively. The success of our method can be appraised by the fact that, if a sequence of 1,000 amino acids is analyzed with our approach, 10 residues will be predicted as NAG-interacting, out of which five are correct. Best models were incorporated in the standalone version and in the webserver available at https://webs.iiitd.edu.in/raghava/nagbinder/.
date: 2020-01-03
volume: 29
issue: 1
is part of: Protein science : a publication of the Protein Society
status: peerReviewed
status: published
author list: authors
type: EPrint
type: ArticleEPrint
is part of: repository
subject: QR Microbiology

Wiley
type: Organization

Protein science : a publication of the Protein Society
type: Collection
issn: 1469896X

Gaurav Mishra
type: Person
given name: Gaurav
family name: Mishra

Rajesh Kumar
type: Person
given name: Rajesh
family name: Kumar

Anjali Dhall
type: Person
given name: Anjali
family name: Dhall

Vinod Kumar
type: Person
given name: Vinod
family name: Kumar

Piyush Agrawal
type: Person
given name: Piyush
family name: Agrawal

Sumeet Patiyal
type: Person
given name: Sumeet
family name: Patiyal

G.P.S. Raghava
type: Person
given name: G.P.S.
family name: Raghava

HTML Summary of #2540 NAGbinder: An approach for identifying N-acetylglucosamine interacting residues of a protein from its primary sequence.
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primary topic: NAGbinder: An approach for identifying N-acetylglucosamine interacting residues of a protein from its primary sequence.

QR Microbiology
type: Concept