Advances of bioinformatics tools applied in virus epitopes prediction

Virologica Sinica

Volumn 26, Issue 1, 2011, Pages 1-7

  Chen, Ping ^a   Rayner, Simon ^a   Hu, Kang Hong ^a  

^a WUHAN INSTITUTE OF VIROLOGY   (China)

Author keywords

Bioinformatics; Epitope; Epitope prediction algorithms

Indexed keywords

EPITOPE; HUMAN METAPNEUMOVIRUS VACCINE; UNCLASSIFIED DRUG; VIRUS VACCINE;

ACCURACY; ALGORITHM; AMINO ACID SEQUENCE; ARTERIVIRUS; ARTICLE; B LYMPHOCYTE; BIOINFORMATICS; COMPUTER MODEL; COMPUTER PROGRAM; CYTOTOXIC T LYMPHOCYTE; DRUG EFFICACY; EPSTEIN BARR VIRUS; FALSE NEGATIVE RESULT; FALSE POSITIVE RESULT; FOOT AND MOUTH DISEASE VIRUS; HUMAN IMMUNODEFICIENCY VIRUS; HUMAN METAPNEUMOVIRUS; HUMAN METAPNEUMOVIRUS INFECTION; INFLUENZA VIRUS A; NONHUMAN; PREDICTION; SENSITIVITY AND SPECIFICITY; SEVERE ACUTE RESPIRATORY SYNDROME; T LYMPHOCYTE; VACCINATION; VIRUS IMMUNITY;

ALGORITHMS; COMPUTATIONAL BIOLOGY; EPITOPES; EPITOPES, B-LYMPHOCYTE; EPITOPES, T-LYMPHOCYTE; VIRUSES;

EID: 79952256874     PISSN: 16740769     EISSN: 1995820X     Source Type: Journal    
DOI: 10.1007/s12250-011-3159-4     Document Type: Article

References (22)

1. M. J. Blythe D. R. Flower 2005 Benchmarking B cell epitope prediction: Underperformance of existing methods Protein Sci 14 1 246 248 1:CAS:528:DC%2BD2MXhtFWrug%3D%3D 10.1110/ps.041059505 15576553 (Pubitemid 40054138)
2. H.H. Bui B. Peters E. Assarsson, et al. 2007 Ab and T cell epitopes of influenza A virus, knowledge and opportunities Proc Natl Acad Sci USA 104 1 246 251 1:CAS:528:DC%2BD2sXjt1OhsA%3D%3D 10.1073/pnas.0609330104 17200302 (Pubitemid 46068017)
3. S. Buus S. L. Lauemøller P. Worning, et al. 2003 Sensitive quantitative predictions of peptide-MHC binding by a 'Query by Committee' artificial neural network approach Tissue Antigens 62 5 378 384 1:CAS:528:DC%2BD3sXpsVOiur0%3D 10.1034/j.1399-0039.2003.00112.x 14617044 (Pubitemid 37345160)
4. M. N. Davies D. R. Flower 2007 Harnessing bioinformatics to discover new vaccines Drug Discov Today 12 9-10 389 395 1:CAS:528:DC%2BD2sXkslahsLk%3D 10.1016/j.drudis.2007.03.010 17467575 (Pubitemid 46636378)
5. I. Díaz J. Pujols L. Ganges, et al. 2009 In silico prediction and ex vivo evaluation of potential T-cell epitopes in glycoproteins 4 and 5 and nucleocapsid protein of genotype-I (European) of porcine reproductive and respiratory syndrome virus Vaccine 27 41 5603 5611 10.1016/j.vaccine.2009.07.029 19646408
6. P. Donnes A. Elofsson 2002 Prediction of MHC class Ibinding peptides, using SVMHC BMC Bioinformatics 3 25 10.1186/1471-2105-3-25 12225620 (Pubitemid 38751179)
7. P. Donnes O. Kohlbacher 2006 SVMHC: a server for prediction of MHC-binding peptides Nucl Acids Res 34 W194 W197 10.1093/nar/gkl284 16844990 (Pubitemid 44529763)
8. P. Guan I. A. Doytchinova C. Zygouri, et al. 2003 MHCPred: bringing a quantitative dimension to the online prediction of MHC binding Appl Bioinformatics 2 1 63 66 1:CAS:528:DC%2BD3sXotVOrtb8%3D 15130834
9. P. Haste Andersen M. Nielsen O. Lund 2006 Prediction of residues in discontinuous B-cell epitopes using protein 3D structures Protein Sci 15 11 2558 2567 10.1110/ps.062405906 17001032 (Pubitemid 44771693)
10. K. A. Herd S. Mahalingam I. M. Mackay, et al. 2006 Cytotoxic T-lymphocyte epitope vaccination protects against human metapneumovirus infection and disease in mice J Virol 80 4 2034 2044 1:CAS:528:DC%2BD28XhsFagsLY%3D 10.1128/JVI.80.4.2034-2044.2006 16439559 (Pubitemid 43228743)
11. B. A. Jameson H. Wolf 1988 The antigenic index: a novel algorithm for predicting antigenic determinants Bioinformatics 4 1 181 186 1:CAS:528:DyaL1cXhvVCkurs%3D 10.1093/bioinformatics/4.1.181 (Pubitemid 18072035)
12. + T cells in a Phase I clinical trial in HIV-uninfected adults Vaccine 27 50 7080 7086 1:CAS:528:DC%2BD1MXhtlCnt7jO 10.1016/j.vaccine.2009.09.060 19786145
13. U. Kulkarni-Kale S. Bhosles A. S. Kolaskar 2005 CEP: a conformational epitope prediction server Nucl Acids Res 33 W168 W171 1:CAS:528: DC%2BD2MXlslyqt70%3D 10.1093/nar/gki460 15980448 (Pubitemid 44529902)
14. J. E. Larsen O. Lund M. Nielsen 2006 Improved method for predicting linear B-cell epitopes Immunome Res 2 2 10.1186/1745-7580-2-2 16635264
15. Y. Lv Z. Ruan L. Wang, et al. 2009 Identification of a novel conserved HLA-A*0201-restricted epitope from the spike protein of SARS-CoV BMC Immunol 10 61 10.1186/1471-2172-10-61 19958537
16. H. Noguchi R. Kato T. Hanai, et al. 2002 Hidden Markov model-based prediction of antigenic peptides that interact with MHC class II molecules J Biosci Bioeng 94 3 264 270 1:CAS:528:DC%2BD38Xptlakt74%3D 16233301 (Pubitemid 35192075)
17. H. Rammensee J. Bachmann N. P. Emmerich, et al. 1999 SYFPEITHI: database for MHC ligands and peptide motifs Immunogenetics 50 3-4 213 219 1:CAS:528:DyaK1MXntlalsbs%3D 10.1007/s002510050595 10602881 (Pubitemid 30099526)
18. S. Saha G. P. Raghava 2006 Prediction of Continuous B-cell Epitopes in an Antigen Using Recurrent Neural Network Proteins 65 1 40 48 1:CAS:528: DC%2BD28Xpt1Cmurk%3D 10.1002/prot.21078 16894596 (Pubitemid 44320614)
19. G. G. Simon Y. Hu A. M. Khan, et al. 2010 Dendritic cell mediated delivery of plasmid DNA encoding LAMP/HIV-1 Gag fusion immunogen enhances T cell epitope responses in HLA DR4 transgenic mice PLoS One 5 1 e8574 10.1371/journal.pone.0008574 20052293
20. H. Singh G. P. Raghava 2001 ProPred: Prediction of HLA-DR binding sites Bioinformatics 17 12 1236 1237 1:CAS:528:DC%2BD38XmtVCksQ%3D%3D 10.1093/bioinformatics/17.12.1236 11751237 (Pubitemid 33735355)
21. + T-Cell Cell Mol Immunol 6 2 97 103 1:CAS:528: DC%2BC3cXjtVSmtbk%3D 10.1038/cmi.2009.13 19403058
22. Z. W. Zhang Y. G. Zhang Y. L. Wang, et al. 2010 Screening and identification of B cell epitopes of structural proteins of foot-and-mouth disease virus serotype Asia1 Vet Microbiol 140 1-2 25 33 1:CAS:528: DC%2BD1MXhsVentL%2FI 10.1016/j.vetmic.2009.07.011 19699594