In silico tools for predicting peptides binding to HLA-class II molecules: More confusion than conclusion

Journal of Proteome Research

Volumn 7, Issue 1, 2008, Pages 154-163

  Gowthaman, Uthaman ^a   Agrewala, Javed N ^a  

^a INSTITUTE OF MICROBIAL TECHNOLOGY   (India)

Author keywords

HLA; Peptide; Promiscuous binders

Indexed keywords

HLA ANTIGEN CLASS 2; HLA DR3 ANTIGEN; PEPTIDE;

ACCURACY; ALLELE; ANTIGEN BINDING; ARTICLE; COMPUTER MODEL; CORRELATION COEFFICIENT; EXPERIMENTATION; PREDICTION; PRIORITY JOURNAL; PROBABILITY; PROTEIN BINDING; RELIABILITY; SENSITIVITY AND SPECIFICITY; VACCINE PRODUCTION;

ANTIGENS; COMPUTATIONAL BIOLOGY; HISTOCOMPATIBILITY ANTIGENS CLASS II; HUMANS; PEPTIDES; PROTEIN BINDING; SOFTWARE; VACCINES;

EID: 38649118833     PISSN: 15353893     EISSN: None     Source Type: Journal    
DOI: 10.1021/pr070527b     Document Type: Article

References (18)

1. Garcia, K. C.; Teyton, L.; Wilson, I. A. Structural basis of T cell recognition. Annu. Rev. Immunol. 1999, 17, 369-97.
2. Maenaka, K.; Jones, E. Y. MHC superfamily structure and the immune system. Curr. Opin. Struct. Biol. 1999, 9 (6), 745-53.
3. Reche, P. A.; Reinherz, E. L. Sequence variability analysis of human class I and class II MHC molecules: functional and structural correlates of amino acid polymorphisms. J. Mol. Biol. 2003, 331 (3), 623-41.
4. Donnes, P.; Kohlbacher, O. SVMHC: a server for prediction of MHC-binding peptides. Nucleic Acids Res. 2006, 34 (Web Server issue), W194-7.
5. Reche, P. A.; Glutting, J. P.; Zhang, H.; Reinherz, E. L. Enhancement to the RANKPEP resource for the prediction of peptide binding to MHC molecules using profiles. Immunogenetics 2004, 56 (6), 405-19.
6. Cui, J.; Han, L. Y.; Lin, H. H.; Tang, Z. Q.; Jiang, L.; Cao, Z. W.; Chen, Y. Z. MHC-BPS: MHC-binder prediction server for identifying peptides of flexible lengths from sequence-derived physico-chemical properties. Immunogenetics 2006, 58 (8), 607-13.
7. Geluk, A.; van Meijgaarden, K. E.; Schloot, N. C.; Drijfhout, J. W.; Ottenhoff, T. H.; Roep, B. O. HLA-DR binding analysis of peptides from islet antigens in IDDM. Diabetes 1998, 47 (10), 1594-601.
8. Texier, C.; Pouvelle, S.; Busson, M.; Herve, M.; Charron, D.; Menez, A.; Maillere, B. HLA-DR restricted peptide candidates for bee venom immunotherapy. J Immunol 2000, 164 (6), 3177-84.
9. Immonen, A.; Farci, S.; Taivainen, A.; Partanen, J.; Pouvelle-Moratille, S.; Narvanen, A.; Kinnunen, T.; Saarelainen, S.; Rytkonen-Nissinen, M.; Maillere, B.; Virtanen, T. T cell epitope-containing peptides of the major dog allergen Can f 1 as candidates for allergen immunotherapy. J. Immunol. 2005, 175 (6), 3614-20.
10. Agrewala, J. N.; Wilkinson, R. J. Influence of HLA-DR on the phenotype of CD4+ T lymphocytes specific for an epitope of the 16-kDa alpha-Crystallin antigen of Mycobacterium tuberculosis. Eur. J. Immunol. 1999, 29 (6), 1753-61.
11. Mandic, M.; Almunia, C.; Vicel, S.; Gillet, D.; Janjic, B.; Coval, K.; Maillere, B.; Kirkwood, J. M.; Zarour, H. M. The alternative open reading frame of LAGE-1 gives rise to multiple promiscuous HLA-DR-restricted epitopes recognized by T-helper 1-type tumor-reactive CD4+ T cells. Cancer Res. 2003, 63 (19), 6506-15.
12. Zarour, H. M.; Maillere, B.; Brusic, V.; Coval, K.; Williams, E.; Pouvelle-Moratille, S.; Castelli, F.; Land, S.; Bennouna, J.; Logan, T.; Kirkwood, J. M. NY-ESO-1 119-143 is a promiscuous major histocompatibility complex class II T-helper epitope recognized by Th1- and Th2-type tumor-reactive CD4+ T cells. Cancer Res. 2002, 62 (1), 213-8.
13. Neumann, F.; Wagner, C.; Stevanovic, S.; Kubuschok, B.; Schormann, C.; Mischo, A.; Ertan, K.; Schmidt, W.; Pfreundschuh, M. Identification of an HLA-DR-restricted peptide epitope with a promiscuous binding pattern derived from the cancer testis antigen HOM-MEL-40/SSX2. Int. J. Cancer 2004, 112 (4), 661-8.
14. Sturniolo, T.; Bono, E.; Ding, J.; Raddrizzani, L.; Tuereci, O.; Sahin, U.; Braxenthaler, M.; Gallazzi, F.; Protti, M. P.; Sinigaglia, F.; Hammer, J. Generation of tissue-specific and promiscuous HLA ligand databases using DNA microarrays and virtual HLA class II matrices. Nat. Biotechnol. 1999, 17 (6), 555-61.
15. Singh, H.; Raghava, G. P. ProPred: prediction of HLA-DR binding sites. Bioinformatics 2001, 17 (12), 1236-7.
16. Guan, P.; Hattotuwagama, C. K.; Doytchinova, I. A.; Flower, D. R. MHCPred 2.0: an updated quantitative T-cell epitope prediction server. Appl. Bioinf. 2006, 5 (1), 55-61.
17. Baldi, P.; Brunak, S.; Chauvin, Y.; Andersen, C. A.; Nielsen, H. Assessing the accuracy of prediction algorithms for classification: an overview. Bioinformatics 2000, 16 (5), 412-24.
18. Bhasin, M.; Raghava, G. P. A hybrid approach for predicting promiscuous MHC class I restricted T cell epitopes. J. Biosci. 2007, 32 (1), 31-42.