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. 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: National Center for Toxicological Research, U.S. Food and Drug Administration, 3900 NCTR Rd, Jefferson, AR 72079 USA.|University of Arkansas at Little Rock/University of Arkansas for Medical Sciences Bioinformatics Graduate Program, 2801 S University Ave, Little Rock, Arkansas, AR 72204 USA.
authors: Heng
authors: H
authors: Luo
authors: National Center for Toxicological Research, U.S. Food and Drug Administration, 3900 NCTR Rd, Jefferson, AR 72079 USA.
authors: Hao
authors: H
authors: Ye
authors: National Center for Toxicological Research, U.S. Food and Drug Administration, 3900 NCTR Rd, Jefferson, AR 72079 USA.
authors: Hui Wen
authors: HW
authors: Ng
authors: National Center for Toxicological Research, U.S. Food and Drug Administration, 3900 NCTR Rd, Jefferson, AR 72079 USA.
authors: Sugunadevi
authors: S
authors: Sakkiah
authors: National Center for Toxicological Research, U.S. Food and Drug Administration, 3900 NCTR Rd, Jefferson, AR 72079 USA.
authors: Donna L
authors: DL
authors: Mendrick
authors: National Center for Toxicological Research, U.S. Food and Drug Administration, 3900 NCTR Rd, Jefferson, AR 72079 USA.
authors: Huixiao
authors: H
authors: Hong
mesh_terms: D000465:Algorithms; D019295:Computational Biology / Q000379:methods; D006680:HLA Antigens / Q000378:metabolism*; D015395:Histocompatibility Antigens Class I / Q000378:metabolism; D006801:Humans; D010455:Peptides / Q000378:metabolism*; D011485:Protein Binding; D015203:Reproducibility of Results
chemical_list: D006680:HLA Antigens; D015395:Histocompatibility Antigens Class I; D010455:Peptides