PEPITO: Improved discontinuous B-cell epitope prediction using multiple distance thresholds and half sphere exposure

Bioinformatics

Volumn 24, Issue 12, 2008, Pages 1459-1460

  Sweredoski, Michael J ^a,b   Baldi, Pierre ^a,b  

^a Irvine   (United States)

^b UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

EPITOPE;

ACCURACY; AMINO ACID ANALYSIS; ANTIGEN ANTIBODY COMPLEX; ARTICLE; B LYMPHOCYTE; CALCULATION; COMPUTER PREDICTION; CONTROLLED STUDY; INTERMETHOD COMPARISON; PRIORITY JOURNAL; PROTEIN STRUCTURE; SCORING SYSTEM; SENSITIVITY AND SPECIFICITY; STRUCTURAL BIOINFORMATICS;

EID: 45449086674     PISSN: 13674803     EISSN: 13674811     Source Type: Journal    
DOI: 10.1093/bioinformatics/btn199     Document Type: Article

References (16)

1. Alix,A.J. (1999) Predictive estimation of protein linear epitopes by using the program PEOPLE. Vaccine, 18, 311-314.
2. Andersen,P. et al. (2006) Prediction of residues in discontinuous B-cell epitopes using protein 3D structures. Protein Sci., 15 2558-2567.
3. Blythe,M.J. and Flower,D.R. (2005) Benchmarking B cell epitope prediction: Underperformance of existing methods. Protein Sci., 14, 246-248.
4. Cheng,J. et al. (2005) SCRATCH: A protein structure and structural feature prediction server. Nucleic Acids Res., 33, w72-w76.
5. Greenbaum,J.A. et al. (2007) Toward a consensus on datasets and evaluation metrics for developing B-cell epitope prediction tools. J. Mol. Recognit., 20, 75-82.
6. Hamelryck,T. (2005) An amino acids has two sides: A new 2D measure provides a different view of solvent exposure. Prot. Struct. Func. Bioinform., 59, 38-48.
7. Hopp,T.P. and Woods,K.R. (1981) Prediction of protein antigenic determinants from amino acid sequences. Proc. Natl Acad. Sci., 78, 3824-3828.
8. Kulkarni-Kale,U. et al. (2005) CEP: A conformational epitope prediction server. Nucleic Acids Res., 33, w168-w171.
9. Larsen,J.E. et al. (2006) Improved method for predicting linear B-cell epitopes. Immunome Res., 2, 2.
10. Mika,S. and Rost,B. (2003) UniqueProt: Creating representative protein-sequence sets. Nucleic Acids Res., 31, 3789-3791.
11. Odorico,M. and Pellequer,J.L. (2003) BEPITOPE: Predicting the location of continuous epitopes and patterns in proteins. J. Mol. Recognit. 16, 20-22.
12. Rapberger,R. et al. (2007) Identification of discontinuous antigenic determinants on proteins based on shape complementarities. J. Mol. Recognit., 20, 113-121.
13. Saha,S. and Raghava,G.P.S. (2006) Prediction of continuous B-cell epitopes in an antigen using recurrent neural networks. Prot. Struct. Funct. Bioinform., 65, 40-48.
14. Schlessinger,A. et al. (2006) Epitome: Database of structure-inferred antigenic epitopes. Nucleic Acids Res., 34 D777-0780.
15. van Regenmortel,M.H. (1996) Mapping epitope structure and activity: From one-dimensional prediction to four-dimensional description of antigenic specificity. Methods, 9, 465-472.
16. van Regenmortel,M.H. (2006) Immunoinformatics may lead to a reappraisal of the nature of B cell epitopes and of the feasibility of synthetic peptide vaccines. J. Mol. Recognit., 19, 183-187.