• MHC Class I Prediction - ANN method
• MHC Class I Prediction - ARB method
• MHC Class I Prediction - SMM method
• MHC Class I Prediction - NetMHCcons method
• MHC Class I Prediction - PickPocket method
• MHC Class II Prediction
• Combined Proteasomal Cleavage/TAP Transport/MHC Class I Predictor
• NetChop and NetCTL
• Scale-Based B Cell Epitope Prediction
• Discotope
• ElliPro
• Population Coverage
• Epitope Conservancy Analysis
• Epitope Cluster Analysis
• Homology Mapping

MHC Class I Prediction - ANN method

Nielsen M, Lundegaard C, Worning P, Lauemoller SL, Lamberth K, Buus S, Brunak S, Lund O. 2003. Reliable prediction of T-cell epitopes using neural networks with novel sequence representations. Protein Sci 12:1007-1017.

MHC Class I Prediction - ARB method

Bui HH, Sidney J, Peters B, Sathiamurthy M, Sinichi A, Purton KA, Mothe BR, Chisari FV, Watkins DI, Sette A. 2005. Automated generation and evaluation of specific MHC binding predictive tools: ARB matrix applications. Immunogenetics 57:304-314.

MHC Class I Prediction - SMM method

Peters B, Sette A. 2005. Generating quantitative models describing the sequence specificity of biological processes with the stabilized matrix method. BMC Bioinformatics 6:132.

MHC Class I Prediction - NetMHCcons method

Karosiene E, Lundegaard C, Lund O and Nielsen M. 2012. NetMHCcons: a consensus method for the major histocompatibility complex class I predictions. Immunogenetics 64(3):177-186

MHC Class I Prediction - PickPocket method

Zhang H, Lund O and Nielsen M. 2009. The PickPocket method for predicting binding specificities for receptors based on receptor pocket similarities: application to MHC–peptide binding. Bioinformatics 25(10):1293–1299.

MHC Class II Prediction

	Bui HH, Sidney J, Peters B, Sathiamurthy M, Sinichi A, Purton KA, Mothe BR, Chisari FV, Watkins DI, Sette A. 2005. Automated generation and evaluation of specific MHC binding predictive tools: ARB matrix applications. Immunogenetics 57:304-314.
	Nielsen M, Lundegaard C, Lund O. 2007. Prediction of MHC class II binding affinity using SMM-align, a novel stabilization matrix alignment method. BMC Bioinformatics 8:238.
	Sturniolo T, Bono E, Ding J, Raddrizzani L, Tuereci O, Sahin U, Braxenthaler M, Gallazzi F, Protti MP, Sinigaglia F, Hammer J. 1999. Generation of tissue-specific and promiscuous HLA ligand databases using DNA microarrays and virtual HLA class II matrices. Nat Biotechnol 17:555-561.

Combined Proteasomal Cleavage/TAP Transport/MHC Class I Predictor

	Tenzer S, Peters B, Bulik S, Schoor O, Lemmel C, Schatz MM, Kloetzel PM, Rammensee HG, Schild H, Holzhutter HG. 2005. Modeling the MHC class I pathway by combining predictions of proteasomal cleavage, TAP transport and MHC class I binding. Cell Mol Life Sci 62:1025-1037.
	Peters B, Bulik S, Tampe R, Van Endert PM, Holzhutter HG. 2003. Identifying MHC class I epitopes by predicting the TAP transport efficiency of epitope precursors. J Immunol171:1741-1749.

NetChop, NetCTL and NetCTLpan

	Nielsen M, Lundegaard C, Lund O, Kesmir C. 2005. The role of the proteasome in generating cytotoxic T-cell epitopes: insights obtained from improved predictions of proteasomal cleavage. Immunogenetics 57:33-41.
	Kesmir C, Nussbaum AK, Schild H, Detours V, Brunak S. 2002. Prediction of proteasome cleavage motifs by neural networks. Protein Eng 15:287-296.
	Larsen MV, Lundegaard C, Lamberth K, Buus S, Brunak S, Lund O, Nielsen M. 2005. An integrative approach to CTL epitope prediction: a combined algorithm integrating MHC class I binding, TAP transport efficiency, and proteasomal cleavage predictions. Eur J Immunol35:2295-2303.
	Nielsen M, Lundegaard C, Worning P, Lauemoller SL, Lamberth K, Buus S, Brunak S, Lund O. 2003. Reliable prediction of T-cell epitopes using neural networks with novel sequence representations. Protein Sci 12:1007-1017.
	Buus S, Lauemoller SL, Worning P, Kesmir C, Frimurer T, Corbet S, Fomsgaard A, Hilden J, Holm A, Brunak S. 2003. Sensitive quantitative predictions of peptide-MHC binding by a 'Query by Committee' artificial neural network approach. Tissue Antigens 62:378-384.
	Peters B, Bulik S, Tampe R, Van Endert PM, Holzhutter HG. 2003. Identifying MHC class I epitopes by predicting the TAP transport efficiency of epitope precursors. J Immunol171:1741-1749.
	Stranzl T, Larsen MV, Lundegaard C, Nielsen M. NetCTLpan: pan-specific MHC class I pathway epitope predictions. Immunogenetics 62:357-68.

Scale-Based B Cell Epitope Prediction

	Chou PY, Fasman GD. 1978. Prediction of the secondary structure of proteins from their amino acid sequence. Adv Enzymol Relat Areas Mol Biol 47:45-148.
	Emini EA, Hughes JV, Perlow DS, Boger J. 1985. Induction of hepatitis A virus-neutralizing antibody by a virus-specific synthetic peptide. J Virol 55:836-839.
	Karplus PA, Schulz GE. 1985. Prediction of chain flexibility in proteins. Naturwissenschaften72:212-213.
	Kolaskar AS, Tongaonkar PC. 1990. A semi-empirical method for prediction of antigenic determinants on protein antigens. FEBS Lett 276:172-174.
	Parker JM, Guo D, Hodges RS. 1986. New hydrophilicity scale derived from high-performance liquid chromatography peptide retention data: correlation of predicted surface residues with antigenicity and X-ray-derived accessible sites. Biochemistry 25:5425-5432.
	Larsen JE, Lund O, Nielsen M. 2006. Improved method for predicting linear B-cell epitopes.Immunome Res 2:2.
	Ponomarenko JV, Bourne PE. 2007. Antibody-protein interactions: benchmark datasets and prediction tools evaluation. BMC Struct Biol 7:64.

Discotope

Haste Andersen P, Nielsen M, Lund O. 2006. Prediction of residues in discontinuous B-cell epitopes using protein 3D structures. Protein Sci 15:2558-2567.

ElliPro

Ponomarenko JV, Bui H, Li W, Fusseder N, Bourne PE, Sette A, Peters B. 2008. ElliPro: a new structure-based tool for the prediction of antibody epitopes. BMC Bioinformatics 9:514

Population Coverage

Bui HH, Sidney J, Dinh K, Southwood S, Newman MJ, Sette A. 2006. Predicting population coverage of T-cell epitope-based diagnostics and vaccines. BMC Bioinformatics 7:153.

Epitope Conservancy Analysis

Bui HH, Sidney J, Li W, Fusseder N, Sette A. 2007. Development of an epitope conservancy analysis tool to facilitate the design of epitope-based diagnostics and vaccines. BMC Bioinformatics 8:361.

Homology Mapping

Beaver JE, Bourne PE, Ponomarenko JV. 2007. EpitopeViewer: a Java application for the visualization and analysis of immune epitopes in the Immune Epitope Database and Analysis Resource (IEDB). Immunome Res 3:3.