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HemoNet : predicting hemolytic activity of peptides with integrated feature learning

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Yaseen, Adiba, Gull, Sadaf, Akhtar, Naeem, Amin, Imran and Minhas, Fayyaz ul Amir Afsar (2021) HemoNet : predicting hemolytic activity of peptides with integrated feature learning. Journal of Bioinformatics and Computational Biology, 19 (5). 2150021. doi:10.1142/S0219720021500219

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Official URL: http://dx.doi.org/10.1142/S0219720021500219

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Abstract

Quantifying the hemolytic activity of peptides is a crucial step in the discovery of novel therapeutic peptides. Computational methods are attractive in this domain due to their ability to guide wet-lab experimental discovery or screening of peptides based on their hemolytic activity. However, existing methods are unable to accurately model various important aspects of this predictive problem such as the role of N/C-terminal modifications, D- and L- amino acids, etc. In this work, we have developed a novel neural network-based approach called HemoNet for predicting the hemolytic activity of peptides. The proposed method captures the contextual importance of different amino acids in a given peptide sequence using a specialized feature embedding in conjunction with SMILES-based fingerprint representation of N/C-terminal modifications. We have analyzed the predictive performance of the proposed method using stratified cross-validation in comparison with previous methods, non-redundant cross-validation as well as validation on external peptides and clinical antimicrobial peptides. Our analysis shows the proposed approach achieves significantly better predictive performance (AUC-ROC of 88%) in comparison to previous approaches (HemoPI and HemoPred with AUC-ROC of 73%). HemoNet can be a useful tool in the search for novel therapeutic peptides. The python implementation of the proposed method is available at the URL: https://github.com/adibayaseen/HemoNet.

Item Type: Journal Article
Subjects: Q Science > QP Physiology
Q Science > QR Microbiology
R Medicine > RM Therapeutics. Pharmacology
Divisions: Faculty of Science, Engineering and Medicine > Science > Computer Science
Library of Congress Subject Headings (LCSH): Hemolysis and hemolysins, Peptides, Anti-infective agents -- Research
Journal or Publication Title: Journal of Bioinformatics and Computational Biology
Publisher: World Scientific Publishing
ISSN: 0219-7200
Official Date: October 2021
Dates:
DateEvent
October 2021Published
5 August 2021Available
26 June 2021Accepted
Volume: 19
Number: 5
Article Number: 2150021
DOI: 10.1142/S0219720021500219
Status: Peer Reviewed
Publication Status: Published
Reuse Statement (publisher, data, author rights): Electronic version of an article published as Journal of Bioinformatics and Computational Biology . 2150021. doi:10.1142/S0219720021500219 © copyright World Scientific Publishing Company https://www.worldscientific.com/worldscinet/jbcb
Access rights to Published version: Restricted or Subscription Access

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