MHC Class I Binding Peptide Prediction Server

References ProPred-I
The Promiscuous MHC Class-I Binding Peptide Prediction Server

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References

Please cite following publication if you are using Propred1:
Singh, H. and Raghava, G. P. S. (2003) ProPred1: Prediction of promiscuous MHC class-I binding sites. Bioinformatics (Accepted)

Following references were used in ProPred1

Ayyoub,M., Stevanovic,S., Sahin,U., Guillaume,P., Servis,C., Rimoldi,D., Valmori,D., Romero,P., Cerottini,J.C., Rammensee,H.G., Pfreundschuh,M., Speiser,D. and Levy,F. (2002) Proteasome-assisted identification of a SSX-2-derived epitope recognized by tumor-reactive CTL infiltrating metastatic melanoma. J. Immunol., 168, 1717-22.

Bhasin,M., Singh,H. and Raghava,G.P.S. (2002) MHCBN: A comprehensive database of MHC binding and non-binding peptides. Nucleic Acid Res., (Online, http://www3.oup.co.uk/nar/database/summary/180.

Craiu,A., Akopian,T., Goldberg,A., and Rock,K.L. (1997) Two distinct proteolytic processes in the generation of a major histocompatibility complex class I-presented peptide. Proc. Natl. Acad. Sci. USA. 94, 10850-55.

Hagmann,M. (2000) Computers aid vaccine design. Science, 290, 80-2.

Holzhutter,H.G., Frommel,C. and Kloetzel,P.M. (1999) A theoretical approach towards the identification of cleavage-determining amino acid motifs of the 20S proteasome. J. Mol. Biol. , 286, 1251-65.

Kessler,J.H., Beekman,N.J., Bres-Vloemans,S.A., Verdijk,P., vanVeelen,P.A., Kloosterman-Joosten,A.M., Vissers,D.C.J., ten Bosch,G.J.A., Kester,M.G.D., Sijts,A., Drijfhout,J.W., Ossendrop,F., Offringa,R. and Melief,C.J.M. (2001) Efficient identification of novel HLA-A*0201-presented cytotoxic T lymphocyte epitopes in the widely expressed tumor antigen PRAME by proteasome-mediated digestion analysis. J. Exp. Med., 193, 73-88.

Kuttler,C., Nussbaum,A.K., Dick,T.P., Rammensee,H.G., Schild,H., and Hadeler,K.P. (2000) An algorithm for the prediction of proteasomal cleavages. J. Mol. Biol., 298, 417-29.

Niedermann,G., Geier,E., Lucchiari-Hartz,M, Hitziger,N., Ramsperger,A. and Eichmann,K. (1999) The specificity of proteasomes: impact on MHC class I processing and presentation of antigens. Immunol. Rev., 127, 29-48.

Nussbaum,A.K., Kuttler,C., Hadeler,K.P., Rammensee,H.G. and Schild,H. (2001) PAProC: a prediction algorithm for proteasomal cleavages available on the WWW. Immunogenetics, 53, 87-94.

Parker,K.C., Bednarek,M.A. and Coligan,J.E. (1994). Scheme for ranking potential HLA-A2 binding peptides based on independent binding of individual peptide side-chains. J Immunol., 152, 163-75.

Rammensee,H., Bachmann,J., Emmerich,N.P., Bachor,O.A. and Stevanovic,S. (1999). SYFPEITHI: database for MHC ligands and peptide motifs. Immunogenetics, 50, 213-9.

Rock,K.H. and Goldberg,A.L. (1999) Degradation of cell proteins and the generation of MHC class I presented peptides. Annu. Rev. Immunol., 17, 739-79.

Ruppert,J., Sidney,J., Celis,E., Kubo,R.T., Grey,H.M. and Sette,A. (1993) Prominent role of secondary anchor residues in peptide binding to HLA-A2.1 molecules. Cell. 74, 929-37.

Sidney,J., Southwood,S., Guercio,M.D., Grey,H.M., Chesnut,R.W., Kubo,R.T. and Sette,A. (1996) Specificity and degeneracy in peptide binding to HLA-B7 like class 1 molecules. J. Immunol., 157, 3480-90.

Singh,H. and Raghava,G.P.S. (2001) ProPred: prediction of HLA-DR binding sites. Bioinformatics, 17, 1236-7.

Stoltze,L., Dick,T.P., Deeg,M., Pommerl,B., Rammensee,H.G. and Schild,H. (1998) Generation of the vesicular stomatitis virus nucleoprotein cytotoxic T lymphocyte epitope requires proteasome-dependent and independent proteolytic activities. Eur. J. Immunol., 28, 4029-36.

Sturniolo,T., Bono,E., Ding,J., Raddrizzani,L., Tuereci,O., Sahin,U., Braxenthaler,M., Gallazzi,F., Protti,M.P., Sinigaglia,F. and Hammer,J. (1999) Generation of tissue-specific and promiscuous HLA ligand database using DNA microarrays and virtual HLA class II matrices. Nat. Biotech., 17, 555-61.

Toes,R.E., Nussbaum,A.K., Degermann,S., Schirle,M., Emmerich,N.P.N., Kraft,M. Laplace,C., Zwinderman,A., Dick,T.P., Muller,J., Schonfisch,B., Schmid,C., Fehling,H.J., Stevanovic,S., Rammensee,H.G., Schild,H. (2001) Discrete cleavage motifs of constitutive and immunoproteasomes revealed by quantitative analysis of cleavage products. J. Exp. Med., 194, 1-12.