This page provides a selection of highly cited historical literature references related to epitope prediction and analysis.

Epitope Informatics' listing in Nature feature articles:

Protein antigenicity

Kolaskar, A.S. and Tongaonkar, P.C. (1990). A semi-empirical method for prediction of antigenic determinants on protein antigens. FEBS Letters, 276: 172-174.

Jameson, B.A. and Wolf, H. (1988). The antigenic index: a novel algorithm for predicting antigenic determinants. Bioinformatics, 4: 181-186.

Parker, J.M.R., Guo, D. and Hodges, R.S. (1986). New hydrophilicity scale derived from high-performance liquid chromatography retention data: correlation of predicted surface residues with antigenicity and X-ray derived accessible sites. Biochemistry, 25, 5425.

Thornton, J.M, Edwards, M.S., Tayler, W.R. and Barlow, D.J. (1986). Location of 'continuous' antigenic determinants in the protruding regions of proteins. EMBO Journal, 5: 409-413.

Welling, G.W., Weijer, W.J., van der Zee, R. and Welling-Wester, S. (1985). Prediction of sequential antigenic regions in proteins. FEBS Letters, 188: 215-218.

Hopp, T.P. and Woods, K.R. (1981). Prediction of protein antigenic determinants from amino acid sequences. Proceedings of the National Academy of Sciences USA, 78: 3824-3828.


Kyte, J. and Doolittle, R.F.(1982). A simple method for displaying the hydropathic character of a protein. Journal of Molecular Biology, 157: 105-132.

Protein hydrophilicity

Engelman, D.M., Steitz, T.A. and Goldman, A. (1986). Identifying nonpolar transmembrane helices in amino acid sequences of membrane proteins. Annual Review of Biophysics and Biophysical Chemistry, 15: 321-353.

Protein hydrophobicity

Cornette, J.L., Cease, K.B., Margalit, H., Spouge, J.L., Berzofsky, J.A. and DeLisi, C. (1987). Hydrophobicity scales and computational techniques for detecting amphipathic structures in proteins. Journal of Molecular Biology, 195: 659-685.

Rose, G.D., Geselowitz, A.R., Lesser, G.J., Lee, R.H. and Zehfus, M.H. (1985) Hydrophobicity of amino acid residues in globular proteins. Science, 229: 834-838.

Fauchere, J.L. and Pliska, V. (1983). Hydrophobic parameters π of amino-acid side chains from the partitioning of N-acetyl-amino-acid amidesEuropean Journal of Medicinal Chemistry (him. Ther.), 18: 369-375.

Sweet, R.M. and Eisenberg, D. (1983). Correlation of sequence hydrophobicities measures similarity in three-dimensional protein structure. Journal of Molecular Biology, 171: 479-488.

Kyte, J. and Doolittle, R.F.(1982). A simple method for displaying the hydropathic character of a protein. Journal of Molecular Biology, 157: 105-132.

Janin, J. (1979). Surface and inside volumes in globular proteins. Nature (London), 277: 491-492.

Manavalan, P. and Ponnuswamy, P.K. (1978). Hydrophobic character of amino acid residues in globular proteins. Nature (London), 275: 673-674.

Protein flexibility

Karplus, P.A. and Schulz, G.E. (1985). Prediction of chain flexibility in proteins: a tool for the selection of peptide antigens. Naturwissenschaften, 72: 212-213.

Vihinen, M., Torkkila, E. and Riikonen, P. (1994). Accuracy of protein flexibility predictions. Proteins: structure, function, and genetics, 19: 141-149.

Westhof, E., Altschuh, D., Moras, D., Bloomer, A.C., Mondragon, A., Klug, A. & Van Regenmortel, M. H. V. (1984). Correlation between segmental mobility and the location of antigenic determinants in proteins. Nature, 311: 123-126.

Protein secondary structure prediction

Garnier, J., Gibrat, J-F. and Robson, B. (1996). GOR method for predicting protein secondary structure from amino acid sequence. Methods Enzymol., 266: 540-553.

Garnier, J., Osguthorpe, D.J. and Robson, B. (1978). Analysis of the accuracy and implications of simple methods for predicting the secondary structure of globular proteins. Journal of Molecular Biology, 120: 97-120.

Chou, P.Y. and Fasman, G.D. (1978). Empirical predictions of protein conformation. Annual Review of Biochemistry, 47: 251-276.

Chou, P.Y. and Fasman, G.D. (1978). Prediction of the secondary structure of proteins from their amino acid sequence. Advances in Enzymology, 47: 45-148.

Chou, P.Y. and Fasman, G.D. (1974). Conformational parameters for amino acids in helical, ß-sheet, and random coil regions calculated from proteins. Biochemistry, 13: 211-222.

Lewis, P.N., Momany, F.A. and Scheraga, H. A. (1971). Folding of polypeptide chains in proteins: a proposed mechanism for folding. Proceedings of the National Academy of Sciences USA, 68: 2293-2297.

B cell epitope prediction reviews

Van Van Regenmortel, M.H.V. (1996). Mapping epitope structure and activity: from one-dimensional prediction to four-dimensional description of antigenic specificity. Methods: a companion to Methods in Enzymology, 9: 465-472.

Pellequer, J.L., Westhof, E. and Van Regenmortel, M.H.V. (1991). Predicting location of continuous epitopes in proteins from their primary structures. Methods in Enzymology, 203: 176-201.

Laver, W.G., Air, G.M., Webster, R.G. and Smith-Gill, S.J. (1990). Epitopes on protein antigens: misconceptions and realities. Cell, 61: 553-556.

Getzoff, E.D., Tainer, J.A., Lerner, R.A. and Geysen, H.M. (1988). The chemistry and mechanism of antibody binding to protein antigens. Advances in Immunology, 43: 1-98.

Hopp, T.P. (1986). Protein surface analysis: methods for identifying antigenic determinants and other interaction sites. Journal of Immunological Methods, 88: 1-18.

T cell epitopes and prediction

Singh, H. and Raghava, G.P.S. (2001) ProPred: prediction of HLA-DR binding sites. Bioinformatics, 17: 1236-1237.

Rammensee, H., Bachmann, J., Emmerich, N.P., Bachor, O.A. and Stevanovic, S. (1999). SYFPEITHI: a database for MHC ligands and peptide motifs. Immunogenetics, 50: 213-219.

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 databases using DNA microarrays and virtual HLA class II matrices. Nature Biotechnology, 17: 555-561.

Brusic, V., Rudy, G., Honeyman, G., Hammer, J. and Harrison, L. (1998). Prediction of MHC class II-binding peptides using an evolutionary algorithm and artificial neural network. Bioinformatics, 14: 121-130.

Honeyman, M.C., Brusic, V., Stone, N.L. and Harrison, L.C. (1998). Neural network-based prediction of candidate T-cell epitopes. Nature Biotechnology, 16: 966-969.

Van den Eynde, B. and van der Bruggen, P. (1997). T cell defined tumour antigens. Current Opinion in Immunology , 9: 684-693.

Rammensee, H-G. (1995). Chemistry of peptides associated with MHC Class I and Class II molecules. Current Opinion in Immunology,7: 85-96.

Meister, G.E., Roberts, C.G.P., Berzofsky, J.A. and De Groot, A.S. (1995). Two novel T cell epitope prediction algorithms based on MHC-binding motifs; comparison of predicted and published epitopes from Mycobacterium tuberculosis and HIV protein sequences. Vaccine, 13: 581-591.

Hammer, J., Bono, E.,  Gallazzi, F., Belunis, C., Nagy, Z. and Sinigaglia, F. (1994). Precise prediction of Major Histocompatibility Complex Class II-peptide interaction based on peptide side chain scanning. Journal of Experimental Medicine, 180: 2353-2358.