AntigenDB: An immunoinformatics database of pathogen antigens

Nucleic Acids Research

Volumn 38, Issue SUPPL.1, 2009, Pages

  Ansari, Hifzur Rahman ^a   Flower, Darren R ^b   Raghava, G P S ^a  

^a INSTITUTE OF MICROBIAL TECHNOLOGY   (India)

^b UNIVERSITY OF OXFORD   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

ANTIGEN; EPITOPE; MAJOR HISTOCOMPATIBILITY ANTIGEN;

AMINO ACID SEQUENCE; ANTIGEN STRUCTURE; ANTIGENDB; ARTICLE; BIOINFORMATICS; DATA BASE; GENE EXPRESSION; IMMUNOINFORMATICS; INFORMATION RETRIEVAL; PEPTIDE MAPPING; PRIORITY JOURNAL; PROTEIN PROCESSING; PROTEIN STRUCTURE; WEB BROWSER; BIOLOGY; CHEMISTRY; COMMUNICABLE DISEASE; COMPUTER PROGRAM; GENETIC DATABASE; HUMAN; IMMUNE SYSTEM; IMMUNOGENETICS; IMMUNOLOGY; INTERNET; LYMPHOCYTE; METABOLISM; METHODOLOGY; PROTEIN DATABASE; PROTEIN TERTIARY STRUCTURE;

ANTIGENS; COMMUNICABLE DISEASES; COMPUTATIONAL BIOLOGY; DATABASES, GENETIC; DATABASES, PROTEIN; EPITOPES; HUMANS; IMMUNE SYSTEM; IMMUNOGENETICS; INFORMATION STORAGE AND RETRIEVAL; INTERNET; LYMPHOCYTES; PEPTIDE MAPPING; PROTEIN PROCESSING, POST-TRANSLATIONAL; PROTEIN STRUCTURE, TERTIARY; SOFTWARE;

EID: 75549090745     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkp830     Document Type: Article

References (28)

1. Pashine, A., Valiante, N.M. and Ulmer, J.B. (2005) Targeting the innate immune response with improved vaccine adjuvants. Nat. Med., 11, S63-S68.
2. Lata, S. and Raghava, G.P.S. (2008) PRRDB: a comprehensive database of Pattern-Recognition Receptors and their ligands. BMC Genomics, 9, 180.
3. Bayry, J., Tchilian, E.Z., Davies, M.N., Forbes, E.K., Draper, S.J., Kaveri, S.V., Hill, A.V., Kazatchkine, M.D., Beverley, P.C., Flower, D.R. et al. (2008) In silico identified CCR4 antagonists target regulatory T cells and exert adjuvant activity in vaccination. Proc. Natl Acad. Sci USA, 105, 10221-10226.
4. Peters, B., Sidney, J., Bourne, P., Bui, H.H., Buus, S., Doh, G., Fleri, W., Kronenberg, M., Kubo, R., Lund, O. et al. (2005) The immune epitope database and analysis resource: from vision to blueprint. PLoS Biol., 3, e91.
5. Bhasin, M., Singh, H. and Raghava, G.P. (2003) MHCBN: a comprehensive database of MHC binding and non-binding peptides. Bioinformatics, 19, 665-666.
6. Toseland, C.P., Clayton, D.J., McSparron, H., Hemsley, S.L., Blythe, M.J., Paine, K., Doytchinova, I.A., Guan, P., Hattotuwagama, C.K. and Flower, D.R. (2005) AntiJen: a quantitative immunology database integrating functional, thermodynamic, kinetic, biophysical, and cellular data. Immunome Res., 1, 4.
7. Saha, S., Bhasin, M. and Raghava, G.P. (2005) Bcipep: a database of B-cell epitopes. BMC Genomics, 6, 79.
8. Boeckmann, B., Bairoch, A., Apweiler, R., Blatter, M.C., Estreicher, A., Gasteiger, E., Martin, M.J., Michoud, K., O'Donovan, C., Phan, I. et al. (2003) The SWISS-PROT protein knowledgebase and its supplement TrEMBL in 2003. Nucleic Acids Res., 31, 365-370.
9. Benson, D.A., Karsch-Mizrachi, I., Lipman, D.J., Ostell, J. and Sayers, E.W. (2009) GenBank. Nucleic Acids Res., 37, D26-D31.
10. Bernstein, F.C., Koetzle, T.F., Williams, G.J., Meyer, E.F. Jr, Brice, M.D., Rodgers, J.R., Kennard, O., Shimanouchi, T. and Tasumi, M. (1977) The Protein Data Bank: a computer-based archival file for macromolecular structures. J. Mol. Biol., 112, 535-542.
11. Barrett, T., Troup, D.B., Wilhite, S.E., Ledoux, P., Rudnev, D., Evangelista, C., Kim, I.F., Soboleva, A., Tomashevsky, M. and Edgar, R. (2007) NCBI GEO: mining tens of millions of expression profiles-database and tools update. Nucleic Acids Res., 35, D760-D765.
12. Ahmad, S., Gromiha, M., Fawareh, H. and Sarai, A. (2004) ASAView: database and tool for solvent accessibility representation in proteins. BMC Bioinformatics, 5, 51.
13. Kopp, J. and Schwede, T. (2004) The SWISS-MODEL Repository of annotated three-dimensional protein structure homology models. Nucleic Acids Res., 32, D230-D234.
14. Kabsch, W. and Sander, C. (1983) Dictionary of protein secondary structure: pattern recognition of hydrogen-bonded and geometrical features. Biopolymers, 22, 2577-2637.
15. Saha, S. and Raghava, G.P.S. (2006) Prediction of continuous B-cell epitopes in an antigen using recurrent neural network. Proteins, 65, 40-48.
16. Guo, T., Hua, S., Ji, X. and Sun, Z. (2004) DBSubLoc: database of protein subcellular localization. Nucleic Acids Res., 32, D122-D124.
17. Rey, S., Acab, M., Gardy, J.L., Laird, M.R., deFays, K., Lambert, C. and Brinkman, F.S. (2005) PSORTdb: a protein subcellular localization database for bacteria. Nucleic Acids Res., 33, D164-D168.
18. Apweiler, R., Attwood, T.K., Bairoch, A., Bateman, A., Birney, E., Biswas, M., Bucher, P., Cerutti, L., Corpet, F., Croning, M.D. et al. (2001) The InterPro database, an integrated documentation resource for protein families, domains and functional sites. Nucleic Acids Res., 29, 37-40.
19. Altschul, S.F., Madden, T.L., Schaffer, A.A., Zhang, J., Zhang, Z., Miller, W. and Lipman, D.J. (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res., 25, 3389-3402.
20. Manoj, S., Babiuk, L.A. and van Drunen Littel-van den Hurk, S. (2004) Approaches to enhance the efficacy of DNA vaccines. Crit. Rev. Clin. Lab. Sci., 41, 1-39.
21. McInerney, J.O. (1998) GCUA: general codon usage analysis. Bioinformatics, 14, 372-373.
22. Lee, T.Y., Huang, H.D., Hung, J.H., Huang, H.Y., Yang, Y.S. and Wang, T.H. (2006) dbPTM: an information repository of protein post-translational modification. Nucleic Acids Res., 34, D622-D627.
23. Diella, F., Cameron, S., Gemund, C., Linding, R., Via, A., Kuster, B., Sicheritz-Ponten, T., Blom, N. and Gibson, T.J. (2004) Phospho.ELM: a database of experimentally verified phosphorylation sites in eukaryotic proteins. BMC Bioinformatics, 5, 79.
24. Garavelli, J.S. (2004) The RESID Database of Protein Modifications as a resource and annotation tool. Proteomics, 4, 1527-1533.
25. Lefranc, M.P., Giudicelli, V., Ginestoux, C., Jabado-Michaloud, J., Folch, G., Bellahcene, F., Wu, Y., Gemrot, E., Brochet, X., Lane, J. et al. (2009) IMGT, the international ImMunoGeneTics information system. Nucleic Acids Res., 37, D1006-D1012.
26. Rammensee, H., Bachmann, J., Emmerich, N.P., Bachor, O.A. and Stevanovic, S. (1999) SYFPEITHI: database for MHC ligands and peptide motifs. Immunogenetics, 50, 213-219.
27. Doytchinova, I.A. and Flower, D.R. (2007) Identifying candidate subunit vaccines using an alignment-independent method based on principal amino acid properties. Vaccine, 25, 856-866.
28. Doytchinova, I.A. and Flower, D.R. (2007) VaxiJen: a server for prediction of protective antigens, tumour antigens and subunit vaccines. BMC Bioinformatics, 8, 4.