Predicting linear B-cell epitopes using amino acid anchoring pair composition

Getzoff ED, Tainer JA, Lerner RA, Geysen HM. The chemistry and mechanism of antibody binding to protein antigens. Adv Immunol. 1988;43:1–98.

Barlow DJ, Edwards MS, Thornton JM. Continuous and discontinuous protein antigenic determinants. Nature. 1986;322:747–8.

Schlessinger A, Ofran Y, Yachdav G, Rost B. Epitome: database of structure-inferred antigenic epitopes. Nucleic Acids Res. 2006;34:D777–80.

Schellekens GA, Visser H, de Jong BA. The diagnostic properties of rheumatoid arthritis antibodies recognizing a cyclic citrullinated peptide. Arthritis Rheum. 2000;43:155–63.

Parker JM, Guo D, Hodges RS. 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. 1986;25:5425–32.

Karplus PA, Schulz GE. Prediction of chain flexibility in proteins - a tool for the selection of peptide antigens. Nature (London). 1985;72:212–3.

Chou PY, Fasman GD. Prediction of the secondary structure of proteins from their amino acid sequence. Adv Enzymol Relat Areas Mol Biol. 1978;47:45–148.

Emini EA, Hughes JV, Perlow DS, Boger J. Induction of hepatitis A virus-neutralizing antibody by a virus-specific synthetic peptide. J Virol. 1985;55:836–9.

Blythe MJ, Flower DR. Benchmarking B cell epitope prediction: underperformance of existing methods. Protein Sci. 2005;14:246–8.

Saha S, Raghava GP. Prediction of continuous B-cell epitopes in an antigen using recurrent neural network. Proteins. 2006;65:40–8.

Chen J, Liu H, Yang J, Chou KC. Prediction of linear B-cell epitopes using amino acid pair antigenicity scale. Amino Acids. 2007;33:423–8.

El-Manzalawy Y, Dobbs D, Honavar V. Predicting linear B-cell epitopes using string kernels. J Mol Recognit. 2008;21:243–55.

Wee LJ, Simarmata D, Kam YW, Nq LF, Tong JC. SVM-based prediction of linear B-Cell epitopes using Bayes Feature Extraction. BMC Genomics. 2010;11(Suppl4):S21.

Singh H, Ansari HR, Raghava GP. Improved method for linear B-cell epitope prediction using antigen's primary sequence. PLoS One. 2013;8, e62216.

Saha S, Bhasin M, Raghava GP. Bcipep: a database of B-cell epitopes. BMC Genomics. 2005;6:79.

Li W, Jaroszewski L, Godzik A. Tolerating some redundancy significantly speeds up clustering of large protein databases. Bioinformatics. 2002;18:77–82.

EL-Manzalawy Y, Dobbs D, Honavar V. Predicting flexible length linear B-cell epitopes, 7th International Conference on Computational Systems Bioinformatics. 2008. p. 121–31.

Bursac Z, Gauss CH, Williams DK, Hosmer DW. Purposeful selection of variables in logistic regression. Source Code Biol Med. 2008;3:17.

Budtz-Jørgensen E, Keiding N, Grandjean P, Weihe P. Confounder selection in environmental epidemiology: assessment of health effects of prenatal mercury exposure. Ann Epidemiol. 2006;17:27–35.

Vapnik V. The Nature of Statistical Learning Theory. Vol. 2. New York, NY, USA: Springer-Verlag New York, Inc; 2000.

Scholkopf B, Sung KK, Burges CJC, Girosi F, Niyogi P, Poggio T, et al. Comparing support vector machines with Gaussian function classifiers. IEEE Trans Sign Proc. 1997;45:2758–65.

Chang CC, Lin CJ. LIBSVM: a library for support vector machines. ACM Trans Intell Syst Technol. 2011;2:27. 1–27.

Doig AJ, Baldwin RL. N- and C-capping preferences for all 20 amino acids in alpha-helical peptides. Protein Sci. 1995;4:1325–36.