caa a22 4500 467907587 CHVBK 20180406152839.0 cr unu---uuuuu 170328e20060801xx s 000 0 eng 10.1007/s00251-006-0117-2 doi (NATIONALLICENCE)springer-10.1007/s00251-006-0117-2 MHC-BPS: MHC-binder prediction server for identifying peptides of flexible lengths from sequence-derived physicochemical properties [Elektronische Daten] [Juan Cui, Lian Han, Hong Lin, Zhi Tang, Li Jiang, Zhi Cao, Yu Chen] Major histocompatibility complex (MHC)-binding peptides are essential for antigen recognition by T-cell receptors and are being explored for vaccine design. Computational methods have been developed for predicting MHC-binding peptides of fixed lengths, based on the training of relatively few non-binders. It is desirable to introduce methods applicable for peptides of flexible lengths and trained by using more diverse sets of non-binders. MHC-BPS is a web-based MHC-binder prediction server that uses support vector machines for predicting peptide binders of flexible lengths for 18 MHC class I and 12 class II alleles from sequence-derived physicochemical properties, which were trained by using 4,208∼3,252 binders and 234,333∼168,793 non-binders, and evaluated by an independent set of 545∼476 binders and 110,564∼84,430 non-binders. The binder prediction accuracies are 86∼99% for 25 and 70∼80% for five alleles, and the non-binder accuracies are 96∼99% for 30 alleles. A screening of HIV-1 genome identifies 0.01∼5% and 5∼8% of the constituent peptides as binders for 24 and 6 alleles, respectively, including 75∼100% of the known epitopes. This method correctly predicts 73.3% of the 15 newly published epitopes in the last 4months of 2005. MHC-BPS is available at http://bidd.cz3.nus.edu.sg/mhc/ . Springer-Verlag, 2006 MHC-binding peptide nationallicence Epitopes nationallicence SVM nationallicence Cui Juan Bioinformatics and Drug Design Group, Department of Pharmacy, National University of Singapore, 117543, Singapore, Singapore aut Han Lian Bioinformatics and Drug Design Group, Department of Pharmacy, National University of Singapore, 117543, Singapore, Singapore aut Lin Hong Bioinformatics and Drug Design Group, Department of Pharmacy, National University of Singapore, 117543, Singapore, Singapore aut Tang Zhi Bioinformatics and Drug Design Group, Department of Pharmacy, National University of Singapore, 117543, Singapore, Singapore aut Jiang Li Bioinformatics and Drug Design Group, Department of Pharmacy, National University of Singapore, 117543, Singapore, Singapore aut Cao Zhi Shanghai Center for Bioinformatics Technology, 100 Qinzhou Road, 200235, Shanghai, People's Republic of China aut Chen Yu Bioinformatics and Drug Design Group, Department of Pharmacy, National University of Singapore, 117543, Singapore, Singapore aut Immunogenetics Springer-Verlag 58/8(2006-08-01), 607-613 0093-7711 58:8<607 2006 58 251 https://doi.org/10.1007/s00251-006-0117-2 text/html Onlinezugriff via DOI 1 research-article jats NATIONALLICENCE 856 40 https://doi.org/10.1007/s00251-006-0117-2 text/html Onlinezugriff via DOI NATIONALLICENCE 700 1- Cui Juan Bioinformatics and Drug Design Group, Department of Pharmacy, National University of Singapore, 117543, Singapore, Singapore aut NATIONALLICENCE 700 1- Han Lian Bioinformatics and Drug Design Group, Department of Pharmacy, National University of Singapore, 117543, Singapore, Singapore aut NATIONALLICENCE 700 1- Lin Hong Bioinformatics and Drug Design Group, Department of Pharmacy, National University of Singapore, 117543, Singapore, Singapore aut NATIONALLICENCE 700 1- Tang Zhi Bioinformatics and Drug Design Group, Department of Pharmacy, National University of Singapore, 117543, Singapore, Singapore aut NATIONALLICENCE 700 1- Jiang Li Bioinformatics and Drug Design Group, Department of Pharmacy, National University of Singapore, 117543, Singapore, Singapore aut NATIONALLICENCE 700 1- Cao Zhi Shanghai Center for Bioinformatics Technology, 100 Qinzhou Road, 200235, Shanghai, People's Republic of China aut NATIONALLICENCE 700 1- Chen Yu Bioinformatics and Drug Design Group, Department of Pharmacy, National University of Singapore, 117543, Singapore, Singapore aut NATIONALLICENCE 773 0- Immunogenetics Springer-Verlag 58/8(2006-08-01), 607-613 0093-7711 58:8<607 2006 58 251 Metadata rights reserved Springer special CC-BY-NC licence nationallicence BK010053 XK010053 XK010000 NATIONALLICENCE NATIONALLICENCE NL-springer