Oct 4, 2007

Antibody-protein interactions: benchmark datasets and prediction tools evaluation

BMC Structural Biology
Julia V Ponomarenko, Philip E Bourne

Abstract

The ability to predict antibody binding sites (aka antigenic determinants or B-cell epitopes) for a given protein is a precursor to new vaccine design and diagnostics. Among the various methods of B-cell epitope identification X-ray crystallography is one of the most reliable methods. Using these experimental data computational methods exist for B-cell epitope prediction. As the number of structures of antibody-protein complexes grows, further interest in prediction methods using 3D structure is anticipated. This work aims to establish a benchmark for 3D structure-based epitope prediction methods. Two B-cell epitope benchmark datasets inferred from the 3D structures of antibody-protein complexes were defined. The first is a dataset of 62 representative 3D structures of protein antigens with inferred structural epitopes. The second is a dataset of 82 structures of antibody-protein complexes containing different structural epitopes. Using these datasets, eight web-servers developed for antibody and protein binding sites prediction have been evaluated. In no method did performance exceed a 40% precision and 46% recall. The values of the area under the receiver operating characteristic curve for the evaluated methods were about 0.6...Continue Reading

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  • Citations82

References

Mentioned in this Paper

Rosaniline Dyes
Protrusion
Twitter Messaging
Muscle Rigidity
Immune System
Cytochrome C Oxidase
Protein Binding
Binding Sites, Antibody
Amino Acids, I.V. solution additive
Complex (molecular entity)

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