{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,12,2]],"date-time":"2025-12-02T15:15:34Z","timestamp":1764688534295},"reference-count":53,"publisher":"Oxford University Press (OUP)","issue":"13","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2006,7,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Motivation: Various computational methods have been proposed to tackle the problem of predicting the peptide binding ability for a specific MHC molecule. These methods are based on known binding peptide sequences. However, current available peptide databases do not have very abundant amounts of examples and are highly redundant. Existing studies show that MHC molecules can be classified into supertypes in terms of peptide-binding specificities. Therefore, we first give a method for reducing the redundancy in a given dataset based on information entropy, then present a novel approach for prediction by learning a predictive model from a dataset of binders for not only the molecule of interest but also for other MHC molecules.<\/jats:p>\n               <jats:p>Results: We experimented on the HLA-A family with the binding nonamers of A1 supertype (HLA-A*0101, A*2601, A*2902, A*3002), A2 supertype (A*0201, A*0202, A*0203, A*0206, A*6802), A3 supertype (A*0301, A*1101, A*3101, A*3301, A*6801) and A24 supertype (A*2301 and A*2402), whose data were collected from six publicly available peptide databases and two private sources. The results show that our approach significantly improves the prediction accuracy of peptides that bind a specific HLA molecule when we combine binding data of HLA molecules in the same supertype. Our approach can thus be used to help find new binders for MHC molecules.<\/jats:p>\n               <jats:p>Contact: \u00a0mami@kuicr.kyoto-u.ac.jp<\/jats:p>\n               <jats:p>Supplementary information: Supplementary data are available at Bioinformatics online.<\/jats:p>","DOI":"10.1093\/bioinformatics\/btl141","type":"journal-article","created":{"date-parts":[[2006,4,14]],"date-time":"2006-04-14T00:35:23Z","timestamp":1144974923000},"page":"1648-1655","source":"Crossref","is-referenced-by-count":29,"title":["Improving MHC binding peptide prediction by incorporating binding data of auxiliary MHC molecules"],"prefix":"10.1093","volume":"22","author":[{"given":"Shanfeng","family":"Zhu","sequence":"first","affiliation":[{"name":"Bioinformatics Center, Institute for Chemical Research, Kyoto University 1 \u00a0 1 \u00a0 \u00a0 Gokasho, Uji 611\u20130011, Japan"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Keiko","family":"Udaka","sequence":"additional","affiliation":[{"name":"Department of Immunology, Kochi Medical School 2 \u00a0 2 \u00a0 \u00a0 Nankoku, Kochi 783\u20138505, Japan"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"John","family":"Sidney","sequence":"additional","affiliation":[{"name":"La Jolla Institute for Allergy and Immunology 3 \u00a0 3 \u00a0 \u00a0 10335 Science Center Drive, La Jolla, CA 92121, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Alessandro","family":"Sette","sequence":"additional","affiliation":[{"name":"La Jolla Institute for Allergy and Immunology 3 \u00a0 3 \u00a0 \u00a0 10335 Science Center Drive, La Jolla, CA 92121, USA"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Kiyoko F.","family":"Aoki-Kinoshita","sequence":"additional","affiliation":[{"name":"Bioinformatics Center, Institute for Chemical Research, Kyoto University 1 \u00a0 1 \u00a0 \u00a0 Gokasho, Uji 611\u20130011, Japan"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Hiroshi","family":"Mamitsuka","sequence":"additional","affiliation":[{"name":"Bioinformatics Center, Institute for Chemical Research, Kyoto University 1 \u00a0 1 \u00a0 \u00a0 Gokasho, Uji 611\u20130011, Japan"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2006,4,13]]},"reference":[{"key":"2023012408322672400_b1","doi-asserted-by":"crossref","first-page":"503","DOI":"10.1172\/JCI119559","article-title":"Human histocompatibility leukocyte antigen-binding supermotifs predict broadly cross-reactive cytotoxic T lymphocyte responses in patients with acute hepatitis","volume":"100","author":"Bertoni","year":"1997","journal-title":"J. Clin. Invest."},{"key":"2023012408322672400_b2","doi-asserted-by":"crossref","first-page":"4447","DOI":"10.4049\/jimmunol.161.8.4447","article-title":"Human class I supertypes and CTL repertoires extend to chimpanzees","volume":"161","author":"Bertoni","year":"1998","journal-title":"J. Immunol."},{"key":"2023012408322672400_b3","doi-asserted-by":"crossref","first-page":"665","DOI":"10.1093\/bioinformatics\/btg055","article-title":"MHCBN: a comprehensive database of MHC binding and non-binding peptides","volume":"19","author":"Bhasin","year":"2003","journal-title":"Bioinformatics"},{"key":"2023012408322672400_b4","doi-asserted-by":"crossref","first-page":"434","DOI":"10.1093\/bioinformatics\/18.3.434","article-title":"JenPep: a database of quantitative functional peptide data for immunology.","volume":"18","author":"Blythe","year":"2002","journal-title":"Bioinformatics"},{"key":"2023012408322672400_b5","doi-asserted-by":"crossref","first-page":"121","DOI":"10.1093\/bioinformatics\/14.2.121","article-title":"Prediction of MHC class II-binding peptides using an evolutionary algorithm and artificial neural network","volume":"14","author":"Brusic","year":"1998","journal-title":"Bioinformatics"},{"key":"2023012408322672400_b6","doi-asserted-by":"crossref","first-page":"368","DOI":"10.1093\/nar\/26.1.368","article-title":"MHCPEP, a database of MHC-binding peptides: update 1997","volume":"26","author":"Brusic","year":"1998","journal-title":"Nucleic Acids Res."},{"key":"2023012408322672400_b7","first-page":"12","article-title":"Data learning: understanding biological data","volume-title":"Knowledge Sharing Across Biological and Medical Knowledge Based Systems: Papers from the 1998 AAAI Workshop","author":"Brusic","year":"1998"},{"key":"2023012408322672400_b8","first-page":"603","article-title":"Data cleaning for computer models: a case study from immunology","author":"Brusic","year":"1999"},{"key":"2023012408322672400_b9","doi-asserted-by":"crossref","first-page":"405","DOI":"10.1016\/S1093-3263(00)00099-1","article-title":"Efficient discovery of immune response targets by cyclical refinement of QSAR models of peptide binding","volume":"19","author":"Brusic","year":"2001","journal-title":"J Mol. Graph Model."},{"key":"2023012408322672400_b10","doi-asserted-by":"crossref","first-page":"280","DOI":"10.1046\/j.1440-1711.2002.01088.x","article-title":"Prediction of promiscuous peptides that bind HLA class I molecules","volume":"80","author":"Brusic","year":"2002","journal-title":"Immunol. Cell Biol."},{"key":"2023012408322672400_b11","doi-asserted-by":"crossref","first-page":"378","DOI":"10.1034\/j.1399-0039.2003.00112.x","article-title":"Sensitive quantitative predictions of peptide-MHC binding by a \u2018Query by Committee\u2019artificial neural network approach","volume":"62","author":"Buus","year":"2003","journal-title":"Tissue Antigens"},{"key":"2023012408322672400_b12","doi-asserted-by":"crossref","first-page":"324","DOI":"10.1007\/s002510050439","article-title":"A geometric study of the amino acid sequence of class I HLA molecules","volume":"48","author":"Cano","year":"1998","journal-title":"Immunogenetics"},{"key":"2023012408322672400_b13","doi-asserted-by":"crossref","first-page":"15","DOI":"10.1007\/s002510050162","article-title":"A roadmap for HLA-A, HLA-B, and HLA-C peptide binding specificities","volume":"45","author":"Chelvanayagam","year":"1996","journal-title":"Immunogenetics"},{"key":"2023012408322672400_b14","doi-asserted-by":"crossref","first-page":"97","DOI":"10.1016\/S1074-7613(00)80513-0","article-title":"Degenerate cytotoxic T cell epitopes from P. falciparum restricted by multiple HLA-A and HLA-B supertype alleles","volume":"7","author":"Doolan","year":"1997","journal-title":"Immunity"},{"key":"2023012408322672400_b15","doi-asserted-by":"crossref","first-page":"25","DOI":"10.1186\/1471-2105-3-25","article-title":"Prediction of MHC class I binding peptides, using SVMHC","volume":"3","author":"D\u00f6nnes","year":"2002","journal-title":"BMC Bioinformatics"},{"key":"2023012408322672400_b16","doi-asserted-by":"crossref","first-page":"4314","DOI":"10.4049\/jimmunol.172.7.4314","article-title":"Identifying human MHC supertypes using bioinformatics methods","volume":"172","author":"Doytchinova","year":"2004","journal-title":"J. Immunol."},{"key":"2023012408322672400_b17","doi-asserted-by":"crossref","first-page":"290","DOI":"10.1038\/351290a0","article-title":"Allele-specific motifs revealed by sequencing of self-peptides eluted from MHC molecules","volume":"351","author":"Falk","year":"1991","journal-title":"Nature"},{"key":"2023012408322672400_b18","doi-asserted-by":"crossref","first-page":"404","DOI":"10.1109\/TC.1977.1674849","article-title":"A recursive partitioning decision rule for non-parametric classification","volume":"26","author":"Friedman","year":"1977","journal-title":"IEEE Trans. Comput."},{"key":"2023012408322672400_b19","doi-asserted-by":"crossref","first-page":"1258","DOI":"10.1006\/jmbi.1997.0937","article-title":"Two complementary methods for predicting peptides binding major histocompatibility complex molecules","volume":"267","author":"Gulukota","year":"1997","journal-title":"J. Mol. Biol."},{"key":"2023012408322672400_b20","doi-asserted-by":"crossref","first-page":"2353","DOI":"10.1084\/jem.180.6.2353","article-title":"Precise prediction of MHC class II-peptide interaction based on peptide side chain scanning","volume":"180","author":"Hammer","year":"1994","journal-title":"J. Exp. Med."},{"key":"2023012408322672400_b21","doi-asserted-by":"crossref","first-page":"669","DOI":"10.1093\/genetics\/133.3.669","article-title":"Contrasting roles of interallelic recombination at the HLA-A and HLA-B loci","volume":"(133)","author":"Hughes","year":"1993","journal-title":"Genetics"},{"key":"2023012408322672400_b22","doi-asserted-by":"crossref","first-page":"257","DOI":"10.1007\/BF00172149","article-title":"Self peptides bound by HLA class I molecules are derived from highly conserved regions of a set of evolutionarily conserved proteins","volume":"41","author":"Hughes","year":"1995","journal-title":"Immunogenetics"},{"key":"2023012408322672400_b23","volume-title":"Immunobiology: The Immune System in Health and Disease.","author":"Janeway","year":"2001"},{"key":"2023012408322672400_b24","doi-asserted-by":"crossref","first-page":"277","DOI":"10.1093\/nar\/gkh063","article-title":"The KEGG resource for deciphering the genome","volume":"32","author":"Kanehisa","year":"2004","journal-title":"Nucleic Acids Res."},{"key":"2023012408322672400_b25","doi-asserted-by":"crossref","first-page":"269","DOI":"10.1146\/annurev.iy.11.040193.001413","article-title":"The molecular descent of the major histocompatibility complex","volume":"11","author":"Klein","year":"1993","journal-title":"Annu. Rev. Immunol."},{"key":"2023012408322672400_b26","doi-asserted-by":"crossref","first-page":"23","DOI":"10.1146\/annurev.iy.08.040190.000323","article-title":"Evolution of class-I MHC genes and proteins: from natural selection to thymic selection","volume":"8","author":"Lawlor","year":"1990","journal-title":"Annu. Rev. Immunol."},{"key":"2023012408322672400_b27","doi-asserted-by":"crossref","first-page":"797","DOI":"10.1007\/s00251-004-0647-4","article-title":"Definition of supertypes for HLA molecules using clustering of specificity matrices","volume":"55","author":"Lund","year":"2004","journal-title":"Immunogenetics"},{"key":"2023012408322672400_b28","doi-asserted-by":"crossref","first-page":"460","DOI":"10.1002\/(SICI)1097-0134(19981201)33:4<460::AID-PROT2>3.0.CO;2-M","article-title":"Predicting peptides that bind to MHC molecules using supervised learning of hidden markov models","volume":"33","author":"Mamitsuka","year":"1998","journal-title":"Proteins."},{"key":"2023012408322672400_b29","doi-asserted-by":"crossref","first-page":"120","DOI":"10.1038\/sj.gene.6363648","article-title":"Taxonomic hierarchy of HLA class I allele sequences","volume":"1","author":"McKenzie","year":"1999","journal-title":"Genes Immun."},{"key":"2023012408322672400_b30","doi-asserted-by":"crossref","first-page":"1388","DOI":"10.1093\/bioinformatics\/bth100","article-title":"Improved prediction of MHC class I and class II epitopes using a novel Gibbs sampling approach","volume":"20","author":"Nielsen","year":"2004","journal-title":"Bioinformatics"},{"key":"2023012408322672400_b31","doi-asserted-by":"crossref","first-page":"4005","DOI":"10.1073\/pnas.85.11.4005","article-title":"Nature of polymorphism in HLA-A, -B, and -C molecules","volume":"85","author":"Parham","year":"1988","journal-title":"Proc. Natl Acad. Sci. USA."},{"key":"2023012408322672400_b32","doi-asserted-by":"crossref","first-page":"163","DOI":"10.4049\/jimmunol.152.1.163","article-title":"Scheme for ranking potential HLA-A2 binding peptides based on independent binding of individual side chain scanning","volume":"152","author":"Parker","year":"1994","journal-title":"J. Immunol."},{"key":"2023012408322672400_b33","doi-asserted-by":"crossref","first-page":"1765","DOI":"10.1093\/bioinformatics\/btg247","article-title":"Examining the independent binding assumption for binding of peptide epitopes to MHC-I molecules","volume":"19","author":"Peters","year":"2003","journal-title":"Bioinformatics"},{"key":"2023012408322672400_b34","first-page":"168","article-title":"Discovering rules by induction from large collections of examples","volume-title":"Expert Systems in the Micro Electronic Age","author":"Quinlan","year":"1979"},{"key":"2023012408322672400_b35","volume-title":"C4.5: Programs for Machine Learning","author":"Quinlan","year":"1993"},{"key":"2023012408322672400_b36","doi-asserted-by":"crossref","first-page":"178","DOI":"10.1007\/BF00172063","article-title":"MHC ligands and peptide motifs: 1st listing","volume":"41","author":"Rammensee","year":"1995","journal-title":"Immunogenetics"},{"key":"2023012408322672400_b37","doi-asserted-by":"crossref","first-page":"213","DOI":"10.1007\/s002510050595","article-title":"SYFPEITHI: database for MHC ligands and peptide motifs","volume":"50","author":"Rammensee","year":"1999","journal-title":"Immunogenetics"},{"key":"2023012408322672400_b38","doi-asserted-by":"crossref","first-page":"701","DOI":"10.1016\/S0198-8859(02)00432-9","article-title":"Prediction of MHC class I binding peptides using profile motifs","volume":"63","author":"Reche","year":"2002","journal-title":"Hum. Immunol."},{"key":"2023012408322672400_b39","first-page":"198","article-title":"Peptide binding at class I MHC scored with linear functions and support vector machines","volume":"15","author":"Riedesel","year":"2004","journal-title":"Gen. Inform."},{"key":"2023012408322672400_b40","doi-asserted-by":"crossref","first-page":"929","DOI":"10.1016\/0092-8674(93)90472-3","article-title":"Prominent role of secondary anchor residues in peptide binding to HLA-A2.1 molecules","volume":"74","author":"Ruppert","year":"1993","journal-title":"Cell"},{"key":"2023012408322672400_b41","doi-asserted-by":"crossref","first-page":"12","DOI":"10.1034\/j.1399-0039.2003.610102.x","article-title":"Population of the HLA ligand database","volume":"61","author":"Sathiamurthy","year":"2003","journal-title":"Tissue Antigens"},{"key":"2023012408322672400_b42","doi-asserted-by":"crossref","first-page":"226","DOI":"10.1093\/nar\/30.1.226","article-title":"FIMM, a database of functional molecular immunology update 2002","volume":"30","author":"Sch\u00f6nbach","year":"2002","journal-title":"Nucleic Acids Res."},{"key":"2023012408322672400_b43","doi-asserted-by":"crossref","first-page":"632","DOI":"10.1111\/j.0006-341X.2001.00632.x","article-title":"Relating amino acid sequence to phenotype: analysis of peptide-binding data","volume":"57","author":"Segal","year":"2001","journal-title":"Biometrics"},{"key":"2023012408322672400_b44","doi-asserted-by":"crossref","first-page":"201","DOI":"10.1007\/s002510050594","article-title":"Nine major HLA class I supertypes account for the vast preponderance of HLA-A and -B polymorphism","volume":"50","author":"Sette","year":"1999","journal-title":"Immunogenetics"},{"key":"2023012408322672400_b45","doi-asserted-by":"crossref","first-page":"830","DOI":"10.1007\/s00251-002-0530-0","article-title":"Class I molecules with similar peptide-binding specificities are the result of both common ancestry and convergent evolution","volume":"54","author":"Sette","year":"2003","journal-title":"Immunogenetics"},{"key":"2023012408322672400_b46","doi-asserted-by":"crossref","first-page":"i297","DOI":"10.1093\/bioinformatics\/bth943","article-title":"Prediction of class I T-cell eptiopes: evidence of presence of immunological hot spots inside antigens","volume":"20","author":"Srinivasan","year":"2004","journal-title":"Bioinformatics"},{"key":"2023012408322672400_b47","doi-asserted-by":"crossref","first-page":"555","DOI":"10.1038\/9858","article-title":"Generation of tissue-specific and promiscuous HLA ligand database using DNA microarrays and virtual HLA class II matrices","volume":"17","author":"Sturniolo","year":"1999","journal-title":"Nat. Biotechnol."},{"key":"2023012408322672400_b48","doi-asserted-by":"crossref","first-page":"2097","DOI":"10.1084\/jem.181.6.2097","article-title":"Decrypting the structure of MHC-I restricted CTL epitopes with complex peptide libraries","volume":"181","author":"Udaka","year":"1995","journal-title":"J Exp. Med."},{"key":"2023012408322672400_b49","doi-asserted-by":"crossref","first-page":"816","DOI":"10.1007\/s002510000217","article-title":"An automated prediction of MHC class I-binding peptides based on positional scanning with peptide libraries","volume":"51","author":"Udaka","year":"2000","journal-title":"Immunogenetics"},{"key":"2023012408322672400_b50","doi-asserted-by":"crossref","first-page":"5744","DOI":"10.4049\/jimmunol.169.10.5744","article-title":"Empirical evaluation of a dynamic experiment design method for prediction of MHC class I-binding peptides","volume":"169","author":"Udaka","year":"2002","journal-title":"J. Immunol."},{"key":"2023012408322672400_b51","doi-asserted-by":"crossref","first-page":"315","DOI":"10.1613\/jair.1199","article-title":"Learning when training data are costly: the effect of class distribution on tree induction","volume":"19","author":"Weiss","year":"2003","journal-title":"J. Artif. Intell. Res."},{"key":"2023012408322672400_b52","doi-asserted-by":"crossref","first-page":"137","DOI":"10.1007\/BF03402006","article-title":"Methods for prediction of peptide binding to MHC molecules: a comparative study","volume":"8","author":"Yu","year":"2002","journal-title":"Mol. Med."},{"key":"2023012408322672400_b53","doi-asserted-by":"crossref","first-page":"929","DOI":"10.1006\/jmbi.1998.1982","article-title":"Structural principles that govern the peptide-binding motifs of class I MHC molecules","volume":"281","author":"Zhang","year":"1998","journal-title":"J. Mol. Biol."}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/22\/13\/1648\/48837855\/bioinformatics_22_13_1648.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/22\/13\/1648\/48837855\/bioinformatics_22_13_1648.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,1,24]],"date-time":"2023-01-24T08:46:02Z","timestamp":1674549962000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/22\/13\/1648\/193717"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2006,4,13]]},"references-count":53,"journal-issue":{"issue":"13","published-print":{"date-parts":[[2006,7,1]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/btl141","relation":{},"ISSN":["1367-4811","1367-4803"],"issn-type":[{"value":"1367-4811","type":"electronic"},{"value":"1367-4803","type":"print"}],"subject":[],"published-other":{"date-parts":[[2006,7,1]]},"published":{"date-parts":[[2006,4,13]]}}}