Bioinformatic requirements for protein database searching using predicted epitopes from disease-associated antibodies

Molecular and Cellular Proteomics

Volumn 7, Issue 2, 2008, Pages 247-256

  Bastas, Gerassimos ^a   Sompuram, Seshi R ^a,b   Pierce, Brian ^c   Vani, Kodela ^b   Bogen, Steven A ^a,b  

^a BOSTON UNIVERSITY SCHOOL OF MEDICINE   (United States)

^b Medical Discovery Partners LLC   (United States)

^c BOSTON UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ANTIBODY; MONOCLONAL ANTIBODY;

ACCURACY; AMINO ACID SEQUENCE; ANTIBODY SPECIFICITY; ARTICLE; BIOINFORMATICS; BIOTECHNOLOGY; CLINICAL EFFECTIVENESS; COMPUTER MODEL; EPITOPE MEDIATED ANTIGEN PREDICTION; MATHEMATICAL ANALYSIS; METHODOLOGY; NUCLEOTIDE SEQUENCE; PATHOPHYSIOLOGY; PREDICTION; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN DATABASE; SEARCH ENGINE; SEQUENCE ANALYSIS; VALIDATION PROCESS;

AMINO ACID MOTIFS; AMINO ACID SEQUENCE; ANTIBODIES; ANTIBODIES, MONOCLONAL; ANTIGENS; BACTERIOPHAGES; COMPUTATIONAL BIOLOGY; CONSENSUS SEQUENCE; DATABASES, PROTEIN; DISEASE; EPITOPES; HUMANS; IMMUNOBLOTTING; MOLECULAR SEQUENCE DATA; PEPTIDES; REPRODUCIBILITY OF RESULTS;

EID: 39749177652     PISSN: 15359476     EISSN: None     Source Type: Journal    
DOI: 10.1074/mcp.M700107-MCP200     Document Type: Article

References (21)

1. Enshell-Seijffers, D., Smelyanski, L., Vardinon, N., Yust, I., and Gershoni, J. (2001) Dissection of the humoral immune response toward an immunoclorninant epitope of HIV: a model for the analysis of antibody diversity in HIV+ individuals. FASEB J. 15,2112-2120
2. Folgori, A., Tafi, R., Meola, A., Felici, F., Galfre, G., Cortese, R., Monaci, P., and Nicosia, A. (1994) A general strategy to identify mimotopes of pathological antigens using only random peptide libraries and human sera. EMBO J. 13, 2236 -2243
3. Scala, G., Chen, X., Liu, W., Noel Telles, J., Cohen, O., Vaccarezza, M., Igarashi, T., and Fauci, A. (1999) Selection of HIV-specific immunogenic epitopes by screening random peptide libraries with HIV-1 positive sera. J. Immunol. 162,6155-6161
4. Prezzi, C., Nuzzo, M., Meola, A., Delmastro, P., Galfre, G., Cortese, R., Nicosia, A., and Monaci, P. (1996) Selection of antigenic and immunogenic mimics of hepatitis C virus using sera from patients. J. Immunol. 156, 4504-4513
5. Wang, L., and Yu, M. (2004) Epitope identification and discovery using phage display libraries: applications in vaccine development and diagnostics. Current Drug Targets 5, 1-15
6. Szecsi, P. B., Riise, E., Roslund, L B., Engberg, J., Turesson, I., Buhl, L., and Schafer-Nielsen, C. (1999) Identification of patient-specific peptides for detection of M-proteins and myeloma cells. Br. J. Haematol. 107,357-364
7. Dybwad, A., Lambin, P., Sioud, M., and Zouali, M. (2003) Probing the specificity of human myeloma proteins with a random peptide phage library. Scand J. Immunol. 57, 583-590
8. Zonder, J., Tainsky, M., Stone, M., Konduri, K., Oliver, J., and Ratner, S. (2005) Myeloma paraprotein epitope identification using a phage library of sterically constrained peptides [Abstract]. American Society of Clinical Oncology Annual Meeting, Orlando, FL
9. Sompuram, S., Bastas, G., Vani, K., and Bogen, S. (2008) Multiple myeloma is commonly derived from HCMV-immunoreactive lymphocytes. Blood 111 302-308
10. McLafferty, M. A., Kent, R. B., Ladner, R. C., and Markland, W. (1993) M13 bacteriophage displaying disulfide-constrained microproteins. Gene 128,29-36
11. Virnekas, B., Ge, L., Pluckthun, A., Schneider, K. C., Wellnhofer, G., and Moroney, S. E. (1994) Trinucleotide phosphoramidites: ideal reagents for the synthesis of mixed oligonucleotides for random mutagenesis. Nucleic Acids Res. 22, 5600-5607
12. Smith, G., and Petrenko, V. (1997) Phage display. Chem. Rev. 97, 391-410
13. Sparks, A., Adey, N., Cwirla, S., and Kay, B. (1996) Screening phage-displayed random peptide libraries. Phage Display of Peptides and Proteins., Academic Press, New York
14. Smith, G. P., and Petrenko, V. A. (1997) Phage display. Chem. Rev. 97, 391-410
15. Bailey, T., and Elkan, C. (1994) Fitting a mixture model by expectation maximization to discover motifs in biopolymers. Proceedings of the Second International Conference on Intelligent Systems for Molecular Biology, pp. 28-36, AAAI Press, Menlo Park, CA
16. Bailey, T. L., Baker, M. E., and Elkan, C. P. (1997) An artificial intelligence approach to motif discovery in protein sequences: application to steroid dehydrogenases. J. Steroid Biochem. Mol. Biol. 62, 29-44
17. Bailey, T., and Gribskov, M. (1998) Combining evidence using p-values: application to sequence homology searches. Bioinformatics 14, 48-54
18. Bailey, T. L., and Gribskov, M. (1998) Methods and statistics for combining motif match scores. J. Comput. Biol. 5, 211-221
19. Sompuram, S. R., Vani, K., Hafer, L. J., and Bogen, S. A. (2006) Antibodies immunoreactive with formalin-fixed tissue antigens recognize linear protein epitopes. Am. J. Clin. Pathol. 125, 82-90
20. Atassi, M. Z. (1984) Antigenic; structures of proteins: their determination has revealed important aspects of immune recognition and generated strategies for synthetic mimiking of protein binding sites. Eur. J. Biochem. 114,1-20
21. Schreiber, A., Humbert, M., Benz, A., and Dietrich, U. (2005) 3D-Epitope-Explorer (3DEX): localization of conformational epitopes within three-dimensional structures of proteins. J. Comput. Chem. 26, 879-887