IEDB

IEDB is a collection of methods to predict linear B cell epitopes based on sequence characteristics of the antigen using amino acid scales and HMMs.


There are 7 methods:

  • Bepipred Linear Epitope Prediction 2.0
  • Bepipred Linear Epitope Prediction
  • Chou & Fasman Beta-Turn Prediction
  • Emini Surface Accessibility Prediction
  • Karplus & Schulz Flexibility Prediction
  • Kolaskar & Tongaonkar Antigenicity
  • Parker Hydrophilicity Prediction

To use IEBD and get more information about methods above, please click here.


Citation:

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.PMID:364941
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. PMID: 2991600
Karplus PA, Schulz GE. 1985. Prediction of chain flexibility in proteins. Naturwissenschaften 72:212-213.PMID: 19055730
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.
Kolaskar AS, Tongaonkar PC. 1990. A semi-empirical method for prediction of antigenic determinants on protein antigens. FEBS Lett276:172-174.PMID: 1702393
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.PMID: 2430611
Larsen JE, Lund O, Nielsen M. 2006. Improved method for predicting linear B-cell epitopes. Immunome Res 2:2.PMID: 16635264
Ponomarenko JV, Bourne PE. 2007. Antibody-protein interactions: benchmark datasets and prediction tools evaluation. BMC Struct Biol 7:64.PMID: 17910770
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.PMID: 17001032
Jespersen MC, Peters B, Nielsen M, Marcatili P. 2017. BepiPred-2.0: improving sequence-based B-cell epitope prediction using conformational epitopes. Nucleic Acids Res (Web Server issue). 2:2.PMID: 28472356