Peptide binding motif predictive algorithms correspond with experimental binding of leukemia vaccine candidate peptides to HLA-A*0201 molecules Journal Article

  

Authors:	Gómez-Nuñez, M.; Pinilla-Ibarz, J.; Dao, T.; May, R. J.; Pao, M.; Jaggi, J. S.; Scheinberg, D. A.
Article Title:	Peptide binding motif predictive algorithms correspond with experimental binding of leukemia vaccine candidate peptides to HLA-A*0201 molecules
Abstract:	The ability to reliably identify the peptides that can bind to MHC molecules is of practical importance for rapid vaccine development. Several computer-based prediction methods have been applied to study the interaction of MHC class I/peptide binding. Here we have compared the binding of peptides predicted by three algorithms (BIMAS, SYFPEITHI and Rankpep) to the binding of the peptides to HLA-A*0201 molecules in vitro, assessed using a MHC stabilization assay on live T2 cells. Fifty HLA-A*0201 peptides were selected from several target oncoproteins: Wilms' tumor protein (WT1), native and imatinib-mutated bcr-abl p210, JAK2 protein and Ewing's sarcoma fusion protein type 1. The sensitivity and specificity of BIMAS, SYFPEITHI and Rankpep respectively, were: 86%, and 82%; 75% and 73%; 64% and 82%. Combining two or more computer methods did not appear to significantly improve the predictive value. © 2006 Elsevier Ltd. All rights reserved.
Keywords:	controlled study; unclassified drug; janus kinase 2; nonhuman; protein motif; accuracy; reproducibility of results; animal cell; unindexed drug; cell line; protein binding; peptide; algorithms; assay; amino acid sequence; cancer vaccine; cancer vaccines; algorithm; peptide fragments; rat; binding sites; bcr abl protein; wt1 protein; major histocompatibility complex; hla a antigen; rna binding protein ews; hla-a antigens; drug protein binding; computer analysis; leukemia vaccine candidate peptides; peptide-mhc class i interaction; predictive computer-based algorithms; alanylleucylleucylleucylarginylthreonylprolyltyrosylserine; alanylleucylleucylleucylarginylthreonylprolyltyrosylvaline; alanylleucylleucylprolylalanylvalylprolylserylleucine; arginylmethionylphenylalanylprolylasparaginylalanylprolyltyrosylleucine; asparaginylleucylglycylalanylthreonylleucyllysylglycylvaline; aspartylleucylasparaginylalanylleucylleucylprolylalanylvaline; cysteinylmethionylthreonyltryptophanylasparaginylglutaminylmethionyl asparaginylleucine; glutamylvalyltyrosylglutamylglycylvalyltryptophanyllysyllysine; glycylleucylarginylarginylglycylisoleucylglutaminylaspartylvaline; glycylvalylphenylalanylarginylglycylisoleucylglutaminylaspartylvaline; lysylarginyltyrosylphenylalanyllysylleucylserylhistidylleucine; lysylleucylglycylglycylglycylglutaminyltyrosylglycylvaline; lysylleucyltyrosylphenylalanyllysylleucylserylhistidylleucine; lysylvalyltyrosylglutamylglycylvalyltryptophanyllysyllysine; serylleucylglycylglutamylglutaminylglutaminyltyrosylserylvaline; tyrosylleucylasparaginylalanylleucylleucylprolylalanylvaline; tyrosylleucylglycylalanylthreonylleucyllysylglycylvaline; tyrosylleucylglycylglutamylglutaminylglutaminyltyrosylserylvaline; tyrosylleucylglycylglycylglycylglutaminyltyrosylglycylvaline; tyrosylleucylleucylprolylalanylvalylprolylserylleucine; tyrosylmethionylphenylalanylprolylasparaginylalanylprolyltyrosylleucine; tyrosylmethionylthreonyltryptophanylasparaginylglutaminylmethionyl asparaginylleucine
Journal Title:	Leukemia Research
Volume:	30
Issue:	10
ISSN:	0145-2126
Publisher:	Elsevier Ltd
Date Published:	2006-10-01
Start Page:	1293
End Page:	1298
Language:	English
DOI:	10.1016/j.leukres.2006.02.010
PUBMED:	16533527
PROVIDER:	scopus
DOI/URL:	http://www.scopus.com/inward/record.url?eid=2-s2.0-33747085478&partnerID=40&md5=ddf93971ffa9d9bb4402caf0af800686
Notes:	--- - "Cited By (since 1996): 18" - "Export Date: 4 June 2012" - "CODEN: LERED" - "Source: Scopus"

https://synapse.mskcc.org/synapse/works/has_related_data_chk/27357