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MULTIPRED: a computational system for prediction of promiscuous HLA binding peptides
1Institute for Infocomm Research 21 Heng Mui Keng Terrace, Singapore 119613 2School of Computer Engineering, Nanyang Technological University Singapore 639798 3Department of Biochemistry, National University of Singapore Singapore 117597 4Department of Pharmacology and Molecular Sciences, Johns Hopkins School of Medicine Baltimore, MD 21205, USA 5Division of Biomedical Sciences Johns Hopkins in Singapore, #02-01 The Nanos, 31 Biopolis Way, Singapore 138669 6School of Land and Food Sciences and the Institute for Molecular Bioscience, University of Queensland Brisbane QLD 4072, Australia
*To whom correspondence should be addressed. Tel: +65 96212 415; Fax: +65 6774 8056; Email: vladimir{at}i2r.a-star.edu.sg
Received February 14, 2005. Revised April 1, 2005. Accepted April 1, 2005.
MULTIPRED is a web-based computational system for the prediction of peptide binding to multiple molecules (proteins) belonging to human leukocyte antigens (HLA) class I A2, A3 and class II DR supertypes. It uses hidden Markov models and artificial neural network methods as predictive engines. A novel data representation method enables MULTIPRED to predict peptides that promiscuously bind multiple HLA alleles within one HLA supertype. Extensive testing was performed for validation of the prediction models. Testing results show that MULTIPRED is both sensitive and specific and it has good predictive ability (area under the receiver operating characteristic curve AROC > 0.80). MULTIPRED can be used for the mapping of promiscuous T-cell epitopes as well as the regions of high concentration of these targets—termed T-cell epitope hotspots. MULTIPRED is available at http://antigen.i2r.a-star.edu.sg/multipred/.
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