IEDB Analysis Resource

IEDB Tools References


MHC Class I Prediction - ANN method

Download PDF 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

Download PDF 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

Download PDF 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.
Download PDF 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.
Download PDF 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.
Download PDF 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.
Download PDF Kesmir C, Nussbaum AK, Schild H, Detours V, Brunak S. 2002. Prediction of proteasome cleavage motifs by neural networks. Protein Eng 15:287-296.
Download PDF 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.
Download PDF 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.
Download PDF 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.
Download PDF 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.
Download PDF 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.
Download PDF 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.
Download PDF Larsen JE, Lund O, Nielsen M. 2006. Improved method for predicting linear B-cell epitopes.Immunome Res 2:2.
Download PDF Ponomarenko JV, Bourne PE. 2007. Antibody-protein interactions: benchmark datasets and prediction tools evaluation. BMC Struct Biol 7:64.

Discotope

Download PDF 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

Download PDF 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

Download PDF 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

Download PDF 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

Download PDF 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.


IEDB       Help       Contact

This site is best viewed with current versions of Mozilla Firefox or Google Chrome.