Epitopia: A web-server for predicting B-cell epitopes

BMC Bioinformatics

Volumn 10, Issue , 2009, Pages 287-

  Rubinstein, Nimrod D ^a   Mayrose, Itay ^b   Martz, Eric ^c   Pupko, Tal ^a  

^a TEL AVIV UNIVERSITY   (Israel)

^b UNIVERSITY OF BRITISH COLUMBIA   (Canada)

^c UNIVERSITY OF MASSACHUSETTS   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

COMPUTATIONAL TOOLS; EPITOPE PREDICTIONS; EXPERIMENTAL APPROACHES; GRAPHICAL INTERFACE; PREDICTIVE POWER; PROTEIN SEQUENCES; PROTEIN STRUCTURES; THREE-DIMENSIONAL STRUCTURE;

EPITOPES; FORECASTING; POLYPEPTIDES; TOOLS;

PROTEINS;

EPITOPE; MEROZOITE SURFACE PROTEIN 1; VASCULOTROPIN;

ACCURACY; ALGORITHM; AMINO ACID SEQUENCE; ARTICLE; CLASSIFIER; COMPUTER GRAPHICS; COMPUTER PREDICTION; CONTROLLED STUDY; IMMUNOGENICITY; INFORMATION SERVICE; MACHINE LEARNING; PLASMODIUM FALCIPARUM; PROBABILITY; PROTEIN STRUCTURE; STRUCTURAL PROTEOMICS; SUPPORT VECTOR MACHINE;

ALGORITHMS; ARTIFICIAL INTELLIGENCE; COMPUTATIONAL BIOLOGY; EPITOPES, B-LYMPHOCYTE; INTERNET; SOFTWARE;

EID: 70449441123     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-10-287     Document Type: Article

References (22)

1. Irving MB, Pan O, Scott JK. Random-peptide libraries and antigen-fragment libraries for epitope mapping and the development of vaccines and diagnostics. Curr Opin Chem Biol 2001, 5(3):314-324. 10.1016/S1367-5931(00)00208-8, 11479124.
2. Westwood OMR, Hay FC. Epitope mapping: a practical approach. 2001, Oxford, UK: Oxford University Press.
3. Jones S, Thornton JM. Analysis of protein-protein interaction sites using surface patches. J Mol Biol 1997, 272(1):121-132. 10.1006/jmbi.1997.1234, 9299342.
4. Lo Conte L, Chothia C, Janin J. The atomic structure of protein-protein recognition sites. J Mol Biol 1999, 285(5):2177-2198. 10.1006/jmbi.1998.2439, 9925793.
5. Chakrabarti P, Janin J. Dissecting Protein-Protein Recognition Sites. Proteins: Structure, Function, and Genetics 2002, 47:334-343.
6. Rubinstein ND, Mayrose I, Halperin D, Yekutieli D, Gershoni JM, Pupko T. Computational characterization of B-cell epitopes. Mol Immunol 2008, 45(12):3477-3489. 10.1016/j.molimm.2007.10.016, 18023478.
7. Saha S, Raghava GP. Prediction of continuous B-cell epitopes in an antigen using recurrent neural network. Proteins 2006, 65(1):40-48. 10.1002/prot.21078, 16894596.
8. Sweredoski MJ, Baldi P. COBEpro: a novel system for predicting continuous B-cell epitopes. Protein Eng Des Sel 2009, 22(3):113-120. 10.1093/protein/gzn075, 19074155.
9. Kulkarni-Kale U, Bhosle S, Kolaskar AS. CEP: a conformational epitope prediction server. Nucleic Acids Res 2005, (33 Web Server):W168-171. 10.1093/nar/gki460, 1160221, 15980448.
10. Haste Andersen P, Nielsen M, Lund O. Prediction of residues in discontinuous B-cell epitopes using protein 3D structures. Protein Sci 2006, 15(11):2558-2567. 10.1110/ps.062405906, 2242418, 17001032.
11. Ponomarenko J, Bui HH, Li W, Fusseder N, Bourne PE, Sette A, Peters B. ElliPro: a new structure-based tool for the prediction of antibody epitopes. BMC Bioinformatics 2008, 9:514. 10.1186/1471-2105-9-514, 2607291, 19055730.
12. Rubinstein ND, Mayrose I, Pupko T. A machine-learning approach for predicting B-cell epitopes. Mol Immunol 2009, 46(5):840-847. 10.1016/j.molimm.2008.09.009, 18947876.
13. Epitopia train data. , http://epitopia.tau.ac.il/trainData
14. Shiryaev SA, Savinov AY, Cieplak P, Ratnikov BI, Motamedchaboki K, Smith JW, Strongin AY. Matrix metalloproteinase proteolysis of the myelin basic protein isoforms is a source of immunogenic peptides in autoimmune multiple sclerosis. PLoS ONE 2009, 4(3):e4952. 10.1371/journal.pone.0004952, 2654159, 19300513.
15. Berman HM, Westbrook J, Feng Z, Gilliland G, Bhat TN, Weissig H, Shindyalov IN, Bourne PE. The protein data bank. Nucleic Acids Res 2000, 28(1):235-242. 10.1093/nar/28.1.235, 102472, 10592235.
16. FirstGlance in Jmol. , http://molvis.sdsc.edu/fgij
17. Sayle RA, Milner-White EJ. RASMOL: biomolecular graphics for all. Trends Biochem Sci 1995, 20(9):374. 10.1016/S0968-0004(00)89080-5, 7482707.
18. Muller YA, Chen Y, Christinger HW, Li B, Cunningham BC, Lowman HB, de Vos AM. VEGF and the Fab fragment of a humanized neutralizing antibody: crystal structure of the complex at 2.4 A resolution and mutational analysis of the interface. Structure 1998, 6(9):1153-1167. 10.1016/S0969-2126(98)00116-6, 9753694.
19. Saha S, Bhasin M, Raghava GP. Bcipep: a database of B-cell epitopes. BMC Genomics 2005, 6(1):79. 10.1186/1471-2164-6-79, 1173103, 15921533.
20. Fawcett T. An introduction to ROC analysis. Pattern Recognition Letters 2006, 27:861-874.
21. Ponomarenko JV, Bourne PE. Antibody-protein interactions: benchmark datasets and prediction tools evaluation. BMC Struct Biol 2007, 7:64. 10.1186/1472-6807-7-64, 2174481, 17910770.
22. Friedman N, Geiger D, Goldszmidt M. Bayesian Network Classifiers. Machine Learning 1997, 29(2-3):131-163.