References

The main reference describing this web site:

A computational resource for the prediction of peptide binding to Indian rhesus macaque MHC class I molecules. Peters B, Bui HH, Sidney J, Weng Z, Loffredo JT, Watkins DI, Mothe BR, Sette A. Vaccine 2005 Nov 1.

A reference describing the algorithm generating the prediction matrices

Generating quantitative models describing the sequence specificity of biological processes with the stabilized matrix method. Peters B. and Sette A. BMC Bioinformatics. 2005 May 31.

The first reference describing the SMM algorithm

Examining the independent binding assumption for binding of peptide epitopes to MHC-I molecules. Peters B, Tong W, Sidney J, Sette A, Weng Z. Bioinformatics. 2003 Sep 22;19(14):1765-72.

Manuscripts describing the experimental data

Identification of seventeen new simian immunodeficiency virus-derived CD8+ T cell epitopes restricted by the high frequency molecule, Mamu-A*02, and potential escape from CTL recognition. Loffredo JT, Sidney J, Wojewoda C, Dodds E, Reynolds MR, Napoe G, Mothe BR, O'Connor DH, Wilson NA, Watkins DI, Sette A. J Immunol. 2004 Oct 15;173(8):5064-76.

Characterization of the peptide-binding specificity of Mamu-A*11 results in the identification of SIV-derived epitopes and interspecies cross-reactivity. Sette A, Sidney J, Bui HH, Del Guercio MF, Alexander J, Loffredo J, Watkins DI, Mothe BR. Immunogenetics. 2005 Mar 4

Characterization of the peptide-binding specificity of Mamu-B*17 and identification of Mamu-B*17-restricted epitopes derived from simian immunodeficiency virus proteins. Mothe BR, Sidney J, Dzuris JL, Liebl ME, Fuenger S, Watkins DI, Sette A. J Immunol. 2002 Jul 1;169(1):210-9.

Definition of the Mamu A*01 peptide binding specificity: application to the identification of wild-type and optimized ligands from simian immunodeficiency virus regulatory proteins. Sidney J, Dzuris JL, Newman MJ, Johnson RP, Kaur A, Amitinder K, Walker CM, Appella E, Mothe B, Watkins DI, Sette A.J Immunol. 2000 Dec 1;165(11):6387-99

CD8(+) lymphocytes from simian immunodeficiency virus-infected rhesus macaques recognize 14 different epitopes bound by the major histocompatibility complex class I molecule mamu-A*01: implications for vaccine design and testing. Allen TM, Mothe BR, Sidney J, Jing P, Dzuris JL, Liebl ME, Vogel TU, O'Connor DH, Wang X, Wussow MC, Thomson JA, Altman JD, Watkins DI, Sette A.J Virol. 2001 Jan;75(2):738-49.