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Title: sNebula, a network-based algorithm to predict binding between human leukocyte antigens and peptides

Abstract

Understanding the binding between human leukocyte antigens (HLAs) and peptides is important to understand the functioning of the immune system. Since it is time-consuming and costly to measure the binding between large numbers of HLAs and peptides, computational methods including machine learning models and network approaches have been developed to predict HLA-peptide binding. However, there are several limitations for the existing methods. We developed a network-based algorithm called sNebula to address these limitations. We curated qualitative Class I HLA-peptide binding data and demonstrated the prediction performance of sNebula on this dataset using leave-one-out cross-validation and five-fold cross-validations. Furthermore, this algorithm can predict not only peptides of different lengths and different types of HLAs, but also the peptides or HLAs that have no existing binding data. We believe sNebula is an effective method to predict HLA-peptide binding and thus improve our understanding of the immune system.

Authors:
 [1];  [2];  [2];  [2];  [2];  [2]
  1. U.S. Food and Drug Administration, Jefferson, AR (United States); Univ. of Arkansas at Little Rock/Univ. of Arkansas for Medical Sciences Bioinformatics Graduate Program, Little Rock, AR (United States)
  2. U.S. Food and Drug Administration, Jefferson, AR (United States)
Publication Date:
Research Org.:
Oak Ridge Inst. for Science and Education (ORISE), Oak Ridge, TN (United States); U.S. Food and Drug Administration, Jefferson, AR (United States). National Center for Toxicological Research
Sponsoring Org.:
USDOE
OSTI Identifier:
1378368
Resource Type:
Journal Article: Accepted Manuscript
Journal Name:
Scientific Reports
Additional Journal Information:
Journal Volume: 6; Journal Issue: 1; Journal ID: ISSN 2045-2322
Publisher:
Nature Publishing Group
Country of Publication:
United States
Language:
English
Subject:
97 MATHEMATICS AND COMPUTING; 60 APPLIED LIFE SCIENCES; MHC; Network topology

Citation Formats

Luo, Heng, Ye, Hao, Ng, Hui Wen, Sakkiah, Sugunadevi, Mendrick, Donna L., and Hong, Huixiao. sNebula, a network-based algorithm to predict binding between human leukocyte antigens and peptides. United States: N. p., 2016. Web. doi:10.1038/srep32115.
Luo, Heng, Ye, Hao, Ng, Hui Wen, Sakkiah, Sugunadevi, Mendrick, Donna L., & Hong, Huixiao. sNebula, a network-based algorithm to predict binding between human leukocyte antigens and peptides. United States. doi:10.1038/srep32115.
Luo, Heng, Ye, Hao, Ng, Hui Wen, Sakkiah, Sugunadevi, Mendrick, Donna L., and Hong, Huixiao. Thu . "sNebula, a network-based algorithm to predict binding between human leukocyte antigens and peptides". United States. doi:10.1038/srep32115. https://www.osti.gov/servlets/purl/1378368.
@article{osti_1378368,
title = {sNebula, a network-based algorithm to predict binding between human leukocyte antigens and peptides},
author = {Luo, Heng and Ye, Hao and Ng, Hui Wen and Sakkiah, Sugunadevi and Mendrick, Donna L. and Hong, Huixiao},
abstractNote = {Understanding the binding between human leukocyte antigens (HLAs) and peptides is important to understand the functioning of the immune system. Since it is time-consuming and costly to measure the binding between large numbers of HLAs and peptides, computational methods including machine learning models and network approaches have been developed to predict HLA-peptide binding. However, there are several limitations for the existing methods. We developed a network-based algorithm called sNebula to address these limitations. We curated qualitative Class I HLA-peptide binding data and demonstrated the prediction performance of sNebula on this dataset using leave-one-out cross-validation and five-fold cross-validations. Furthermore, this algorithm can predict not only peptides of different lengths and different types of HLAs, but also the peptides or HLAs that have no existing binding data. We believe sNebula is an effective method to predict HLA-peptide binding and thus improve our understanding of the immune system.},
doi = {10.1038/srep32115},
journal = {Scientific Reports},
number = 1,
volume = 6,
place = {United States},
year = {Thu Aug 25 00:00:00 EDT 2016},
month = {Thu Aug 25 00:00:00 EDT 2016}
}

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Cited by: 3 works
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Works referenced in this record:

Amino acid substitution matrices from protein blocks.
journal, November 1992

  • Henikoff, S.; Henikoff, J. G.
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