title: Machine Learning Methods for Predicting HLA-Peptide Binding Activity.
abstract: As major histocompatibility complexes in humans, the human leukocyte antigens (HLAs) have important functions to present antigen peptides onto T-cell receptors for immunological recognition and responses. Interpreting and predicting HLA-peptide binding are important to study T-cell epitopes, immune reactions, and the mechanisms of adverse drug reactions. We review different types of machine learning methods and tools that have been used for HLA-peptide binding prediction. We also summarize the descriptors based on which the HLA-peptide binding prediction models have been constructed and discuss the limitation and challenges of the current methods. Lastly, we give a future perspective on the HLA-peptide binding prediction method based on network analysis.
authors.affiliation: National Center for Toxicological Research, U.S. Food and Drug Administration, Jefferson, AR, USA. ; University of Arkansas at Little Rock/University of Arkansas for Medical Sciences Bioinformatics Graduate Program, Little Rock, AR, USA.
authors.forename: Heng
authors.initials: H
authors.lastname: Luo
authors.affiliation: National Center for Toxicological Research, U.S. Food and Drug Administration, Jefferson, AR, USA.
authors.forename: Hao
authors.initials: H
authors.lastname: Ye
authors.affiliation: National Center for Toxicological Research, U.S. Food and Drug Administration, Jefferson, AR, USA.
authors.forename: Hui Wen
authors.initials: HW
authors.lastname: Ng
authors.affiliation: Center for Pharmacogenomics, School of Pharmacy, Fudan University, Shanghai, China.
authors.forename: Leming
authors.initials: L
authors.lastname: Shi
authors.affiliation: National Center for Toxicological Research, U.S. Food and Drug Administration, Jefferson, AR, USA.
authors.forename: Weida
authors.initials: W
authors.lastname: Tong
authors.affiliation: National Center for Toxicological Research, U.S. Food and Drug Administration, Jefferson, AR, USA.
authors.forename: Donna L
authors.initials: DL
authors.lastname: Mendrick
authors.affiliation: National Center for Toxicological Research, U.S. Food and Drug Administration, Jefferson, AR, USA.
authors.forename: Huixiao
authors.initials: H
authors.lastname: Hong
keywords: HLA; MHC; binding; machine learning; peptide; prediction