ElliPro: A new structure-based tool for the prediction of antibody epitopes

BMC Bioinformatics

Volumn 9, Issue , 2008, Pages

  Ponomarenko, Julia ^a,b   Bui, Huynh Hoa ^a,c   Li, Wei ^a,b   Fusseder, Nicholas ^a,b   Bourne, Philip E ^a,b   Sette, Alessandro ^d   Peters, Bjoern ^d  

^a UNIVERSITY OF CALIFORNIA   (United States)

^b UNIVERSITY OF CALIFORNIA   (United States)

^c ISIS PHARMACEUTICALS   (United States)

^d LA JOLLA INSTITUTE FOR ALLERGY AND IMMUNOLOGY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BENCHMARK DATASETS; EPITOPE PREDICTIONS; GEOMETRICAL PROPERTY; IMMUNODIAGNOSTICS; PROTEIN SEQUENCES; PROTEIN STRUCTURES; PROTEIN-PROTEIN INTERACTIONS; SOLVENT ACCESSIBILITY;

ANTIBODIES; CLUSTERING ALGORITHMS; FORECASTING; TOOLS;

EPITOPES;

ANTIBODY; PROTEIN; EPITOPE;

ACCESS TO INFORMATION; ACCURACY; AMINO ACID SEQUENCE; AREA UNDER THE CURVE; ARTICLE; COMPUTER PROGRAM; EPITOPE MAPPING; INTERMETHOD COMPARISON; INTERNET; MEDICAL RESEARCH; PREDICTION; PROTEIN PROTEIN INTERACTION; PROTEIN STRUCTURE; QUALITY CONTROL; SENSITIVITY AND SPECIFICITY; STRUCTURE ANALYSIS; ALGORITHM; ANTIBODY COMBINING SITE; BIOLOGICAL MODEL; BIOLOGY; CHEMISTRY; CLUSTER ANALYSIS; COMPUTER INTERFACE; GENETICS; HUMAN; METHODOLOGY; PROTEIN CONFORMATION; SEQUENCE ANALYSIS;

ALGORITHMS; BINDING SITES, ANTIBODY; CLUSTER ANALYSIS; COMPUTATIONAL BIOLOGY; EPITOPE MAPPING; EPITOPES, B-LYMPHOCYTE; HUMANS; INTERNET; MODELS, IMMUNOLOGICAL; PROTEIN CONFORMATION; SEQUENCE ANALYSIS, PROTEIN; SOFTWARE; USER-COMPUTER INTERFACE;

EID: 58049187138     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-9-514     Document Type: Article

References (22)

1. Peters B Sidney J Bourne P Bui HH Buus S Doh G Fleri W Kronenberg M Kubo R Lund O et al. The design and implementation of the immune epitope database and analysis resource Immunogenetics 2005, 57(5):326-336. 15895191 10.1007/s00251-005-0803-5
2. Bijker MS Melief CJ Offringa R Burg van der SH Design and development of synthetic peptide vaccines: Past, present and future Expert Rev Vaccines 2007, 6(4):591-603. 17669012 10.1586/14760584.6.4.591
3. Gomara MJ Haro I Synthetic peptides for the immunodiagnosis of human diseases Curr Med Chem 2007, 14(5):531-546. 17346145 10.2174/ 092986707780059698
4. Greenbaum JA Andersen PH Blythe M Bui HH Cachau RE Crowe J Davies M Kolaskar AS Lund O Morrison S et al. Towards a consensus on datasets and evaluation metrics for developing B-cell epitope prediction tools J Mol Recognit 2007, 20(2):75-82. 17205610 10.1002/jmr.815
5. Laver WG Air GM Webster RG Smith-Gill SJ Epitopes on protein antigens: misconceptions and realities Cell 1990, 61(4):553-556. 1693095 10.1016/ 0092-8674(90)90464-P
6. Van Regenmortel MHV Mapping Epitope Structure and Activity: From One-Dimensional Prediction to Four-Dimensional Description of Antigenic Specificity Methods 1996, 9(3):465-472. 8812702 10.1006/meth.1996.0054
7. Westhof E Altschuh D Moras D Bloomer AC Mondragon A Klug A Van Regenmortel MH Correlation between segmental mobility and the location of antigenic determinants in proteins Nature 1984, 311(5982):123-126. 6206398 10.1038/311123a0
8. Novotny J Handschumacher M Haber E Bruccoleri RE Carlson WB Fanning DW Smith JA Rose GD Antigenic determinants in proteins coincide with surface regions accessible to large probes (antibody domains) Proc Natl Acad Sci USA 1986, 83(2):226-230. 2417241 10.1073/pnas.83.2.226 322830
9. Thornton JM Edwards MS Taylor WR Barlow DJ Location of 'continuous' antigenic determinants in the protruding regions of proteins EMBO J 1986, 5(2):409-413. 1166746 2423325
10. Eswar NWB Marti-Renom MA Madhusudhan MS Eramian D Shen MY Pieper U Sali A Comparative Protein Structure Modeling With MODELLER Current Protocols in Bioinformatics. 5.6.1-5.6.30 John Wiley & Sons, Inc 2006 Supplement 15
11. Ponomarenko JV Bourne PE Antibody-protein interactions: Benchmark datasets and prediction tools evaluation BMC Struct Biol 2007, 7:64. 17910770 10.1186/1472-6807-7-64 2174481
12. Kulkarni-Kale U Bhosle S Kolaskar AS CEP: A conformational epitope prediction server Nucleic Acids Res 2005 33(Web Server issue):W168-171. 15980448 10.1093/nar/gki460 1160221
13. 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. 17001032 10.1110/ps.062405906 2242418
14. Mandell JG Roberts VA Pique ME Kotlovyi V Mitchell JC Nelson E Tsigelny I Ten Eyck LF Protein docking using continuum electrostatics and geometric fit Protein Eng 2001, 14(2):105-113. 11297668 10.1093/protein/ 14.2.105
15. Schneidman-Duhovny D Inbar Y Polak V Shatsky M Halperin I Benyamini H Barzilai A Dror O Haspel N Nussinov R et al. Taking geometry to its edge: Fast unbound rigid (and hinge-bent) docking Proteins 2003, 52(1):107-112. 12784375 10.1002/prot.10397
16. Bradford WD Jr Improved prediction of protein-protein binding sites using a support vector machines approach Bioinformatics 2005, 21(8):1487-94. 10.1093/bioinformatics/bti242 15613384
17. Neuvirth H Raz R Schreiber G ProMate: A structure based prediction program to identify the location of protein-protein binding sites J Mol Biol 2004, 338(1):181-199. 15050833 10.1016/j.jmb.2004.02.040
18. 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. 10592235 10.1093/nar/28.1.235 102472
19. Altschul SF Gish W Miller W Myers EW Lipman DJ Basic local alignment search tool J Mol Biol 1990, 215(3):403-410. 2231712
20. Taylor WR Thornton JM Turnell WG An ellipsoidal approximation of protein shape Journal of Molecular Graphics 1983, 1:30-38. 10.1016/ 0263-7855(83)80001-0
21. Jmol http://jmol.sourceforge.net
22. Fawcett T An introduction to ROC analysis Pattern Recognition Letters 2006, 27:861-874. 10.1016/j.patrec.2005.10.010