Computational prediction of B cell epitopes from antigen sequences

Methods in Molecular Biology

Volumn 1184, Issue , 2014, Pages 197-215

  Gao, Jianzhao ^a   Kurgan, Lukasz ^b  

^a NANKAI UNIVERSITY   (China)

^b UNIVERSITY OF ALBERTA   (Canada)

Author keywords

Antigen; B cell epitope; Conformational epitope; Database; Immunotherapeutic; Linear epitope; Prediction; Vaccine

Indexed keywords

ANTIGEN; B CELL EPITOPE; EPITOPE; UNCLASSIFIED DRUG;

AMINO ACID SEQUENCE; ANTIGENICITY; ARTICLE; B LYMPHOCYTE; CONFORMATION; HEART DEVELOPMENT; HYDROPHILICITY; HYDROPHOBICITY; PREDICTION; PRIORITY JOURNAL; PROTEIN DATABASE; PROTEIN SECONDARY STRUCTURE; SUPPORT VECTOR MACHINE; ANIMAL; BIOLOGY; CHEMISTRY; HUMAN; IMMUNOLOGY; INFORMATION PROCESSING; PROCEDURES; PROTEIN CONFORMATION;

ANIMALS; ANTIGENS; COMPUTATIONAL BIOLOGY; DATASETS AS TOPIC; EPITOPES, B-LYMPHOCYTE; HUMANS; PROTEIN CONFORMATION;

EID: 84925884639     PISSN: 10643745     EISSN: None     Source Type: Book Series    
DOI: 10.1007/978-1-4939-1115-8_11     Document Type: Article

References (66)

1. Kringelum JV, Lundegaard C, Lund O, Nielsen M (2012) Reliable B cell epitope predictions: impacts of method development and improved benchmarking. PLoS Comput Biol 8(12): e1002829
2. Pellequer JL, Westhof E, van Regenmortel MH (1991) Predicting location of continuous epitopes in proteins from their primary structures. Methods Enzymol 203:176-201
3. Reineke U, Schutkowski M (2009) Epitope mapping protocols. Methods Mol Biol, vol 524
4. El-Manzalawy Y, Honavar V (2010) Recent advances in B-cell epitope prediction methods. Immunome Res 6(Suppl 2):S2
5. Yao B, Zheng D, Liang S, Zhang C (2013) Conformational B-cell epitope prediction on antigen protein structures: a review of current algorithms and comparison with common binding site prediction methods. PLoS One 8(4):e62249
6. Ansari HR, Raghava GP (2013) In silico models for B-cell epitope recognition and signaling. Methods Mol Biol 993:129-138
7. Yang X, Yu X (2009) An introduction to epitope prediction methods and software. Rev Med Virol 19(2):77-96
8. Vita R, Zarebski L, Greenbaum JA, Emami H, Hoof I, Salimi N, Damle R, Sette A, Peters B (2010) The immune epitope database 2.0. Nucleic Acids Res 38:D854-D862
9. Sharma OP, Das AA, Krishna R, Kumar SM, Mathur PP (2012) Structural Epitope Database (SEDB): a Web-based database for the epitope, and its intermolecular interaction along with the tertiary structure information. J Proteomics Bioinform 5:84-89
10. Toseland CP, Clayton DJ, McSparron H, Hemsley SL, Blythe MJ, Paine K, Doytchinova AI, Guan P, Hattotuwagama CK, Flower DR (2005) AntiJen: a quantitative immunology database integrating functional, thermodynamic, kinetic, biophysical, and cellular data. Immunome Res 1:4
11. Kim Y, Ponomarenko J, Zhu Z, Tamang D, Wang P, Greenbaum J, Lundegaard C, Sette A, Lund O, Bourne PE, Nielsen M, Peters B (2012) Immune epitope database analysis resource. Nucleic Acids Res 40:W525-W530
12. Zhang Q, Wang P, Kim Y, Haste-Andersen P, Beaver J, Bourne PE, Bui HH, Buus S, Frankild S, Greenbaum J, Lund O, Lundegaard C, Nielsen M, Ponomarenko J, Sette A, Zhu Z, Peters B (2008) Immune epitope database analysis resource (IEDB-AR). Nucleic Acids Res 36:W513-W518
13. Rubinstein ND, Mayrose I, Martz E, Pupko T (2009) Epitopia: a web-server for predicting B-cell epitopes. BMC Bioinformatics 10:287
14. Rubinstein ND, Mayrose I, Pupko T (2009) A machine-learning approach for predicting B-cell epitopes. Mol Immunol 46:840-847
15. Gao J, Faraggi E, Zhou Y, Ruan J, Kurgan L (2012) BEST: improved prediction of B-cell epitopes from antigen sequences. PLoS One 7:e40104
16. Blythe MJ, Doytchinova IA, Flower DR (2002) JenPep: a database of quantitative functional peptide data for immunology. Bioinformatics 18:434-439
17. McSparron H, Blythe MJ, Zygouri C, Doytchinova IA, Flower DR (2003) JenPep: a novel computational information resource for immunobiology and vaccinology. J Chem Inf Comput Sci 43:1276-1287
18. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ (1990) Basic local alignment search tool. J Mol Biol 215(3):403-410
19. Peters B, Sidney J, Bourne P, Bui HH, Buus S, Doh G, Fleri W, Kronenberg M, Kubo R, Lund O, Nemazee D, Ponomarenko JV, Sathiamurthy M, Schoenberger S, Stewart S, Surko P, Way S, Wilson S, Sette A (2005) The immune epitope database and analysis resource: from vision to blueprint. PLoS Biol 3(3):e91
20. Peters B, Sette A (2007) Integrating epitope data into the emerging web of biomedical knowledge resources. Nat Rev Immunol 7(6): 485-490
21. Saha S, Bhasin M, Raghava GP (2005) Bcipep: a database of B-cell epitopes. BMC Genomics 6(1):79
22. Huang J, Honda W (2006) CED: a conformational epitope database. BMC Immunol 7:7
23. Schlessinger A, Ofran Y, Yachdav G, Rost B (2006) Epitome: database of structure-inferred antigenic epitopes. Nucleic Acids Res 34: D777-D780
24. Berman HM, Westbrook J, Feng Z, Gilliland G, Bhat TN, Weissig H, Shindyalov IN, Bourne PE (2000) The protein data bank. Nucleic Acids Res 28(1):235-242
25. Laskowski RA (2001) PDBsum: summaries and analyses of PDB structures. Nucleic Acids Res 29:221-222
26. Bhasin M, Singh H, Raghava GP (2003) MHCBN: a comprehensive database of MHC binding and non-binding peptides. Bioinformatics 19:665-666
27. Kaas Q, Ruiz M, Lefranc MP (2004) IMGT/3Dstructure-DB and IMGT/ StructuralQuery, a database and a tool for immunoglobulin, T cell receptor and MHC structural data. Nucleic Acids Res 32: D208-D210
28. Magrane M, UniProt Consortium (2011) UniProt Knowledgebase: a hub of integrated protein data. Database:bar009
29. Pruitt KD, Tatusova T, Brown GR, Maglott DR (2012) NCBI Reference Sequences (RefSeq): current status, new features and genome annotation policy. Nucleic Acids Res 40:D130-D135
30. Hopp TP, Woods KR (1981) Prediction of protein antigenic determinants from amino acid sequences. Proc Natl Acad Sci U S A 78: 3824-3828
31. Welling GW, Weijer WJ, van der Zee R, Welling-Wester S (1985) Prediction of sequential antigenic regions in proteins. FEBS Lett 188:215-218
32. Karplus PA, Schulz GE (1985) Prediction of chain flexibility in proteins: a tool for the selection of peptide antigen. Naturwissenschaften 72:212-213
33. Parker JM, Guo D, Hodges RS (1986) New hydrophilicity scale derived from highperformance liquid chromatography peptide retention data: correlation of predicted surface residues with antigenicity and X-ray derived accessible sites. Biochemistry 25:5425-5432
34. Kolaskar AS, Tongaonkar PC (1990) A semi empirical method for prediction of antigenic determinants on protein antigens. FEBS Lett 276:172-174
35. Pellequer JL, Westhof E, van Regenmortel MH (1993) Correlation between the location of antigenic sites and the prediction of turns in proteins. Immunol Lett 36(1):83-99
36. Pellequer JL, Westhof E (1993) PREDITOP: a program for antigenicity prediction. J Mol Graph 11:191-202
37. Alix AJ (1999) Predictive estimation of protein linear epitopes by using the program PEOPLE. Vaccine 18:311-314
38. Odorico M, Pellequer JL (2003) BEPITOPE: predicting the location of continuous epitopes and patterns in proteins. J Mol Recognit 16(1): 20-22
39. Saha S, Raghava GP (2004) BcePred: prediction of continuous b-cell epitopes in antigenic sequences using physico-chemical properties. Third Intern Conf on Artifi cial Immune Systems. pp 197-204
40. Chang HT, Liu CH, Pai TW (2008) Estimation and extraction of B-cell linear epitopes predicted by mathematical morphology approaches. J Mol Recognit 21(6):431-441
41. Blythe MJ, Flower D (2005) Benchmarking B cell epitope prediction: underperformance of existing methods. Protein Sci 14:246-248
42. Saha S, Raghava GP (2006) Prediction of continuous B-cell epitopes in an antigen using recurrent neural network. Proteins 65(1):40-48
43. Larsen JE, Lund O, Nielsen M (2006) Improved method for predicting linear B-cell epitopes. Immunome Res 2:2
44. Chen J, Liu H, Yang J, Chou KC (2007) Prediction of linear B-cell epitopes using amino acid pair antigenicity scale. Amino Acids 33(3): 423-428
45. El-Manzalawy Y, Dobbs D, Honavar V (2008) Predicting linear B-cell epitopes using string kernels. J Mol Recognit 21(4):243-255
46. El-Manzalawy Y, Dobbs D, Honavar V (2008) Predicting flexible length linear B-cell epitopes. Comput Syst Bioinformatics Conf 7:121-132
47. Sweredoski MJ, Baldi P (2009) COBEpro: a novel system for predicting continuous B-cell epitopes. Protein Eng Des Sel 22(3):113-120
48. Wee LJ, Simarmata D, Kam YW, Ng LF, Tong JC (2010) SVM-based prediction of linear B-cell epitopes using Bayes feature extraction. BMC Genomics 11(Suppl 4):S21
49. Wang Y, Wu W, Negre NN, White KP, Li C, Shah PK (2011) Determinants of antigenicity and specifi city in immune response for protein sequences. BMC Bioinformatics 12:251
50. Wang HW, Lin YC, Pai TW, Chang HT (2011) Prediction of B-cell linear epitopes with a combination of support vector machine classification and amino acid propensity identification. J Biomed Biotechnol 2011:432830
51. Yao B, Zhang L, Liang S, Zhang C (2012) SVMTriP: a method to predict antigenic epitopes using support vector machine to integrate tri-peptide similarity and propensity. PLoS One 7(9):e45152
52. Singh H, Ansari HR, Raghava GP (2013) Improved method for linear B-cell epitope prediction using antigens primary sequence. PLoS One 8(5):e62216
53. Altschul SF, Madden TL, Schäffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 25(17):3389-3402
54. Jones DT (1999) Protein secondary structure prediction based on position-specific scoring matrices. J Mol Biol 292(2):195-202
55. Cheng J, Randall AZ, Sweredoski MJ, Baldi P (2005) SCRATCH: a protein structure and structural feature prediction server. Nucleic Acids Res 33:W72-W76
56. Vucetic S, Brown CJ, Dunker AK, Obradovic Z (2003) Flavors of protein disorder. Proteins 52:573-584
57. Wootton JC, Federhen S (1996) Analysis of compositionally biased regions in sequence databases. Methods Enzymol 266:554-571
58. Ansari HR, Raghava GP (2010) Identification of conformational B-cell epitopes in an antigen from its primary sequence. Immunome Res 6:6
59. Zhang W, Niu Y, Xiong Y, Zhao M, Yu R, Liu J (2012) Computational prediction of conformational B-cell epitopes from antigen primary structures by ensemble learning. PLoS One 7(8):e43575
60. Pollastri G, Baldi P, Fariselli P, Casadio R (2002) Prediction of coordination number and relative solvent accessibility in proteins. Proteins 47(2):142-153
61. Pollastri G, Przybylski D, Rost B, Baldi P (2002) Improving the prediction of protein secondary structure in three and eight classes using recurrent neural networks and profiles. Proteins 47(2):228-235
62. Faraggi E, Xue B, Zhou Y (2009) Improving the prediction accuracy of residue solvent accessibility and real-value backbone torsion angles of proteins by guided-learning through a twolayer neural network. Proteins 74:847-856
63. Dor O, Zhou Y (2007) Achieving 80 % tenfold cross-validated accuracy for secondary structure prediction by large-scale training. Proteins 66:838-845
64. Adamczak R, Porollo A, Meller J (2005) Combining prediction of secondary structure and solvent accessibility in proteins. Proteins 59:467-475
65. Wang P, Sidney J, Dow C, Mothé B, Sette A, Peters B (2008) A systematic assessment of MHC class II peptide binding predictions and evaluation of a consensus approach. PLoS Comput Biol 4(4):e1000048
66. Moutaftsi M, Peters B, Pasquetto V, Tscharke DC, Sidney J, Bui HH, Grey H, Sette A (2006) A consensus epitope prediction approach identifi es the breadth of murine T(CD8+)-cell responses to vaccinia virus. Nat Biotechnol 24(7):817-819