title: NIEluter: Predicting peptides eluted from HLA class I molecules.
abstract: The immune system has evolved to make a diverse repertoire of peptides processed from self and foreign proteomes, which are displayed in antigen-binding grooves of major histocompatibility complex (MHC) proteins at cell surface for surveillance by T cells. These antigenic peptides are termed Naturally Processed Peptides or Naturally Presented Peptides (NPPs), which play a major role in cell-mediated immunity and rational vaccine design. Therefore, it is intensely desirable to predict NPPs from a given protein antigen, or to foretell if an MHC-binding peptide can be eluted from a given MHC protein. In this paper, we describe NIEluter, an ensemble predictor based on support vector machine (SVM). It consists of a combination of five SVM models trained with position-specific amino acid composition, position-specific dipeptide composition, Hidden Markov Model, binary encoding, and BLOSUM62 feature. NIEluter can predict NPPs of length 8-11 from six HLA alleles (A0201, B0702, B3501, B4403, B5301, and B5701) at present. Evaluated with five-fold cross-validation and independent datasets if available, NIEluter shows good performance. It outperforms MHC-NP in 7 out of 24 types of situation and precedes NetMHC3.2 in most cases, indicating that it is a helpful complement to available tools. NIEluter has been implemented as a free web service, which can be accessed at http://immunet.cn/nie/cgi-bin/nieluter.pl.
authors: Center of Bioinformatics (COBI), Key Laboratory for NeuroInformation of Ministry of Education, University of Electronic Science and Technology of China, Chengdu 610054, China.
authors: Qiang
authors: Q
authors: Tang
authors: Center of Bioinformatics (COBI), Key Laboratory for NeuroInformation of Ministry of Education, University of Electronic Science and Technology of China, Chengdu 610054, China.
authors: Fulei
authors: F
authors: Nie
authors: Center of Bioinformatics (COBI), Key Laboratory for NeuroInformation of Ministry of Education, University of Electronic Science and Technology of China, Chengdu 610054, China.
authors: Juanjuan
authors: J
authors: Kang
authors: Center of Bioinformatics (COBI), Key Laboratory for NeuroInformation of Ministry of Education, University of Electronic Science and Technology of China, Chengdu 610054, China; Center for Information in Biomedicine, University of Electronic Science and Technology of China, Chengdu 610054, China.
authors: Hui
authors: H
authors: Ding
authors: Center of Bioinformatics (COBI), Key Laboratory for NeuroInformation of Ministry of Education, University of Electronic Science and Technology of China, Chengdu 610054, China; Center for Information in Biomedicine, University of Electronic Science and Technology of China, Chengdu 610054, China.
authors: Peng
authors: P
authors: Zhou
authors: Center of Bioinformatics (COBI), Key Laboratory for NeuroInformation of Ministry of Education, University of Electronic Science and Technology of China, Chengdu 610054, China; Center for Information in Biomedicine, University of Electronic Science and Technology of China, Chengdu 610054, China.
authors: Jian
authors: J
authors: Huang
mesh_terms: D000465:Algorithms; D015395:Histocompatibility Antigens Class I / Q000276:immunology*; D006801:Humans; D007111:Immunity, Cellular / Q000276:immunology; D008390:Markov Chains; D010455:Peptides / Q000276:immunology; D011485:Protein Binding / Q000276:immunology; D060388:Support Vector Machine; D013601:T-Lymphocytes / Q000276:immunology
chemical_list: D015395:Histocompatibility Antigens Class I; D010455:Peptides
keywords: HLA class I molecules; Immune system; NPPs; Support vector machine