{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2024,7,2]],"date-time":"2024-07-02T22:40:55Z","timestamp":1719960055107},"reference-count":45,"publisher":"Oxford University Press (OUP)","issue":"4","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2006,2,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Motivation: The MHC superfamily (MhcSF) consists of immune system MHC class I (MHC-I) proteins, along with proteins with a MHC-I-like structure that are involved in a large variety of biological processes. \u03b22-Microglobulin (B2M) non-covalent binding to MHC-I proteins is required for their surface expression and function, whereas MHC-I-like proteins interact, or not, with B2M. This study was designed to predict B2M binding (or non-binding) of newly identified MhcSF proteins, in order to decipher their function, understand the molecular recognition mechanisms and identify deleterious mutations. IMGT standardization of MhcSF protein domains provides a unique numbering of the multiple alignment positions, and conditions to develop such predictive tool.<\/jats:p>\n               <jats:p>Method: We combine a simple-Bayes classifier with IMGT unique numbering. Our method involves two steps: (1) selection of discriminant binary features, which associate an alignment position with an amino acid group; and (2) learning of the classifier by estimating the frequencies of selected features, conditionally to the B2M binding property.<\/jats:p>\n               <jats:p>Results: Our dataset contains aligned sequences of 806 allelic forms of 47 MhcSF proteins, corresponding to 9 receptor types and 4 mammalian species. Eighteen discriminant features are selected, belonging to B2M contact sites, or stabilizing the molecular structure required for this contact. Three leave-one-out procedures are used to assess classifier performance, which corresponds to B2M binding prediction for: (1) new proteins, (2) species not represented in the dataset and (3) new receptor types. The prediction accuracy is high, i.e. 98, 94 and 70%, respectively. Application of our classifier to lower vertebrate MHC-I proteins indicates that these proteins bind to B2M and should then be expressed on the cellular surface by a process similar to that of mammalian MHC-I proteins. These results demonstrate the usefulness and accuracy of our (simple) approach, which should apply to other function or interaction prediction problems.<\/jats:p>\n               <jats:p>Availability: Data and MhcSF multiple alignments are available on the IMGT website ().<\/jats:p>\n               <jats:p>Contact: \u00a0gascuel@lirmm.fr, duprat@ligm.igh.cnrs.fr, lefranc@ligm.igh.cnrs.fr<\/jats:p>\n               <jats:p>Supplementary information: Supplementary material is downloadable at .<\/jats:p>","DOI":"10.1093\/bioinformatics\/bti826","type":"journal-article","created":{"date-parts":[[2005,12,14]],"date-time":"2005-12-14T02:28:47Z","timestamp":1134527327000},"page":"453-459","source":"Crossref","is-referenced-by-count":16,"title":["A simple method to predict protein-binding from aligned sequences\u2014application to MHC superfamily and \u03b22-microglobulin"],"prefix":"10.1093","volume":"22","author":[{"given":"Elodie","family":"Duprat","sequence":"first","affiliation":[{"name":"Laboratoire d'ImmunoG\u00e9n\u00e9tique Mol\u00e9culaire 1 \u00a0 1 \u00a0 \u00a0 IGH (UPR CNRS 1142), 141 rue de la Cardonille, 34396 Montpellier Cedex 5, France"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Marie-Paule","family":"Lefranc","sequence":"additional","affiliation":[{"name":"Laboratoire d'ImmunoG\u00e9n\u00e9tique Mol\u00e9culaire 1 \u00a0 1 \u00a0 \u00a0 IGH (UPR CNRS 1142), 141 rue de la Cardonille, 34396 Montpellier Cedex 5, France"},{"name":"Institut Universitaire de France 2 \u00a0 2 \u00a0 \u00a0 103 Boulevard Saint-Michel, 75005 Paris, France"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Olivier","family":"Gascuel","sequence":"additional","affiliation":[{"name":"Projet M\u00e9thodes et Algorithmes pour la Bioinformatique 3 \u00a0 3 \u00a0 \u00a0 LIRMM (UMR CNRS-UM2 5506), 161 rue Ada, 34392 Montpellier Cedex 5, France"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2005,12,13]]},"reference":[{"key":"2023012408503344400_b1","doi-asserted-by":"crossref","first-page":"303","DOI":"10.1007\/s002510050497","article-title":"MHC class I genes of the channel catfish: sequence analysis and expression","volume":"49","author":"Antao","year":"1999","journal-title":"Immunogenetics"},{"key":"2023012408503344400_b2","article-title":"Predicting protein-ligand interactions from primary structure","volume-title":"Technical Report TR02-398","author":"Bandyopadhyay","year":"2002"},{"key":"2023012408503344400_b3","doi-asserted-by":"crossref","first-page":"1329","DOI":"10.1084\/jem.166.5.1329","article-title":"Site-directed mutagenesis of class I HLA genes. 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