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A substantial revision of references is planned to occur late 2010.
Protein antigenicity prediction algorithms Hopp and
Woods Protein hydrophobicity algorithms Fauchere Protein hydrophilicity algorithms Goldman, Engelman and
Steitz (GES) Protein flexibility prediction algorithm Karplus and Schulz Protein secondary structure prediction algorithms GOR II & IV methods (Garnier
and Robson) B cell epitope prediction reviews 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. (1994). Epitope predictions from the primary structure of proteins. In Peptide antigens: a practical approach (ed. G.B. Wisdom), pp. 7-25. Oxford University Press, Oxford. Carter, J.M. (1994). Epitope prediction methods. In Methods in Molecular Biology (ed. B.M. Dunn and M.W. Pennington), Vol. 36, pp. 193-206. Human Press Inc., New Jersey. Van Regenmortel, M.H.V. (1992). Molecular dissection of protein antigens. In Structure of antigens (ed. M.H.V. Van Regenmortel), Vol. 1, pp. 1-27. CRC Press, Boca Raton. Stern, P.S. (1991). Predicting antigenic sites on proteins. Trends in Biotechnology, 9: 163-169. 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. Hopp, T.P. (1989). Use of hydrophilicity plotting procedures to identify protein antigenic segments and other interaction sites. Methods in Enzymology, 178: 571-585. Van Regenmortel, M.H.V. (1989). The concept and operational definition of protein epitopes. Philosophical Transactions of the Royal Society of London, 323: 451-466. 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. Van Regenmortel, M.H.V. and de Marcillac, G.D. (1988). An assessment of prediction methods for locating continuous epitopes in proteins. Immunology Letters, 17: 95-108. Hopp, T.P. (1986). Protein surface analysis: methods for identifying antigenic determinants and other interaction sites. Journal of Immunological Methods, 88: 1-18. Van Regenmortel, M.H.V.
(1986). Which structural features determine protein antigenicity? Trends
in Biochemical Sciences, 11: 36-39. Other B cell epitope prediction Alix, A.J.P. (2000). Predictive estimation of protein linear epitopes by using the program PEOPLE. Vaccine, 18: 311-314.
Vihinen, M., Torkkila, E. and Riikonen, P. (1994). Accuracy of protein flexibility predictions. Proteins: structure, function, and genetics, 19: 141-149. Maksyutov, A.Z. and Zagrebelnaya, E.S. (1993). ADEPT: a computer program for prediction of protein antigenic determinants. Bioinformatics, 9: 291-297.
Hofmann, H-J., Hädge, D., Höltje, M. and Höltje, H-D. (1991). Theoretical prediction of antigenic determinants based on protein-water interaction energies. Quantitative Structure-Activity Relationships, 10: 300-305. Hofmann, H-J., Hädge, D., Höltje, M. and Höltje, H-D. (1990). Protein-water interaction energies as predictor for antigenic determinants. Molecular Immunology, 27: 1057-1060. Krchñák, V., Mach, O. and Malý, A. (1989). Computer prediction of B-cell determinants from protein amino acid sequences based on incidence of b turns. Methods in Enzymology, 178: 586-611. Stern, P.S. (1989). Normal-mode dynamics as a tool for predicting antigenic sites on proteins. Progress in Clinical Biological Research, 289: 87-94. Jameson, B.A. and Wolf, H. (1988). The antigenic index: a novel algorithm for predicting antigenic determinants. Bioinformatics, 4: 181-186. 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
Sequence Database Searches - BLAST Altschul, S.F., Warren, G., Miller, W.,
Myers, E.W. and Lipman, D.J. (1990). Basic local alignment search tool.
Journal of Molecular Biology, 215: 403-410. Sequence Retrieval Searches - Entrez Benson, D.A., Boguski, M.S., Lipman, D.J.,
Ostell, J., Ouellette, B.F.F., Rapp, B.A., Wheeler, D.L. (1999). GenBank.
Nucleic Acids Research, 27: 12-17. Sequence Database Searches - PROSITE Bairoch, A., Bucher, P. and Hofmann, K. (1997). The PROSITE database, its status in 1997. Nucleic Acids Research, 25: 217-221. Attwood, T.K. and Parry-Smith, D.J. (2001). Introduction to bioinformatics. Prentice Hall, New Jersey.
Bioinformatics: genes, proteins and computers. Eds Orengo, C.A., Jones, D.T. and Thornton, J.M., BIOS Scientific Publishers Ltd, Oxford, 2003.
Peri, S.,
Ibarrola, N., Mann, M. and Pandey, A. (2001). Common pitfalls in
bioinformatics-based analyses: look before you leap. Trends in Genetics,
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Kwok, W.W., Gebe, J.A., Liu, A., Agar, S., Ptacek, N., Hammer, J., Koelle, D.M. and Nepom, G.T. (2001). Rapid epitope identification from complex class-II-restricted T-cell antigens. Trends in Immunology, 22: 583-588.
Mallios, R.R. (2001). Predicting class II MHC/peptide multilevel binding with an iterative stepwise discriminative analysis meta-algorithm. Bioinformatics, 17: 942-948. Römisch, K. (2001). How antigenic peptides are made to fit their groove. Trends in Biochemical Sciences, 26: 531. Schirle, M., Weinschenk, T. and Stevanovic, S. (2001). Combining computer algorithms with experimental approaches permits the rapid and accurate identification of T cell epitopes from defined antigens. Journal of Immunological Methods, 257: 1-16. Singh, H. and Raghava, G.P.S. (2001) ProPred: prediction of HLA-DR binding sites. Bioinformatics, 17: 1236-1237. Andersen, M.H., Tan, L., Søndergaard, I., Zeuthen, J., Elliott, T. and Haurum, J.S. (2000). Poor correspondence between predicted and experimental binding of peptides to class I MHC molecules. Tissue Antigens, 55: 519-531. Buus, S. (1999). Description and prediction of peptide-MHC binding: the 'human MHC project'. Current Opinion in Immunology, 11: 209-213. De Groot, A.S. and Rothman, F.G. (1999). In silico predictions; in vivo veritas. Nature Biotechnology, 17: 533-534. Mallios, R.R. (1999). Class II quantitative binding motifs derived from a large molecular database with a versatile iterative stepwise discriminative analysis meta-algorithm. Bioinformatics, 15: 432-439. Pinilla, C., Martin, R., Gran, B., Appel, J.R., Boggiano, C., Wilson, D.B. and Houghten, R.A. (1999). Exploring immunological specificity using synthetic peptide combinatorial libraries. Current Opinion in Immunology, 11: 193-202.
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. Maffei, A. and Harris, P.E. (1998). Peptides bound to major histocompatibility complex molecules. Peptides, 19: 179-198. Hammer, J., Sturniolo, T. and Sinigaglia, F. (1997). HLA class II binding specificity and autoimmunity. Advances in Immunology, 66: 67-100. Van den Eynde, B. and van der Bruggen, P. (1997). T cell defined tumour antigens. Current Opinion in Immunology, 9: 684-693. Wilson, I.A. and Garcia, K.C. (1997). T-cell receptor structure and TCR complexes. Current Opinion in Structural Biology, 7: 839-848. Walden, P. (1996). T-cell epitope determination. Current Opinion in Immunology, 8: 68-74. Deavin, A.J., Auton, T.R. and Greaney, P.J. (1996). Statistical comparison of established T-cell epitope predictors against a large database of human and murine antigens. Molecular Immunology, 33: 145-155. Saavedra, R., Beccerril, M.A., Dubeaux, C., Lippens, R., De Vos, M-J., Herion, P. and Bollen, A. (1996). Epitopes recognised by human T lymphocytes in the ROP2 protein antigen of Toxoplasma gondii. Infection and immunity, 64: 3858-3862. es three algorithms for T cell epitope prediction) Rammensee, H-G. (1995). Chemistry of peptides associated with MHC Class I and Class II molecules. Current Opinion in Immunology, 7: 85-96. Hammer, J., Gallazzi, F. and Sinigaglia, F. (1995). Molecular understanding of MHC peptide binding specificity and prediction of T-cell epitopes. Periodicum Biologorum, 98: 155-158. Davenport, M.P., Ho Shon, I.A.P. and Hill, A.V.S. (1995). An empirical method for the prediction of T-cell epitopes. Immunogenetics, 42: 392-397. 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. (1995). New methods to predict MHC-binding sequences within protein antigens. Current Opinion in Immunology, 7: 263-269. Rötzschke, O. and Falk, K. (1994). Origin, structure and motifs of naturally processed MHC class II ligands. Current Opinion in Immunology, 6: 45-51. 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. Sinigaglia, F. and Hammer, J. (1994). Defining rules for the peptide-MHC class II interaction. Current Opinion in Immunology, 6: 52-56. Hobohm, U. and Meyerhans, A. (1993). A pattern search method for putative anchor residues in T cell epitopes. European Journal of Immunology, 23: 1271-1276. Reyes, V.E., Lew, R.A., Lu, S. and Humphreys, R.E. (1991). Prediction of a helices and T cell-presented sequences in proteins with algorithms based on strip-of-helix hydrophobicity index. Methods in Enzymology, 202: 225-238.Menédez-Arias, L. and Rodríguez, R. (1990). A BASIC microcomputer program for prediction of B and T cell epitopes in proteins. Bioinformatics, 6: 101-105.
Cornette, J.L., Margalit, H., DeLisi, C. and Berzofsky, J.A. (1989). Identification of T-cell epitopes and use in construction of synthetic vaccines. Methods in Enzymology, 178: 611-634. Stille, C.J., Thomas, L.J., Reyes, V.E. and Humphreys, R.E. (1987). Hydrophobic strip-of-helix algorithm for selection of T cell-presented peptides. Molecular Immunology, 24: 1021-1027.
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