Back to Search
Start Over
Antibody-specified B-cell epitope prediction in line with the principle of context-awareness.
- Source :
-
IEEE/ACM transactions on computational biology and bioinformatics [IEEE/ACM Trans Comput Biol Bioinform] 2011 Nov-Dec; Vol. 8 (6), pp. 1483-94. - Publication Year :
- 2011
-
Abstract
- Context-awareness is a characteristic in the recognition between antigens and antibodies, highlighting the reconfiguration of epitope residues when an antigen interacts with a different antibody. A coarse binary classification of antigen regions into epitopes, or nonepitopes without specifying antibodies may not accurately reflect this biological reality. Therefore, we study an antibody-specified epitope prediction problem in line with this principle. This problem is new and challenging as we pinpoint a subset of the antigenic residues from an antigen when it binds to a specific antibody. We introduce two kinds of associations of the contextual awareness: 1) residues-residues pairing preference, and 2) the dependence between sets of contact residue pairs. Preference plays a bridging role to link interacting paratope and epitope residues while dependence is used to extend the association from one-dimension to two-dimension. The paratope/epitope residues' relative composition, cooperativity ratios, and Markov properties are also utilized to enhance our method. A nonredundant data set containing 80 antibody-antigen complexes is compiled and used in the evaluation. The results show that our method yields a good performance on antibody-specified epitope prediction. On the traditional antibody-ignored epitope prediction problem, a simplified version of our method can produce a competitive, sometimes much better, performance in comparison with three structure-based predictors.
Details
- Language :
- English
- ISSN :
- 1557-9964
- Volume :
- 8
- Issue :
- 6
- Database :
- MEDLINE
- Journal :
- IEEE/ACM transactions on computational biology and bioinformatics
- Publication Type :
- Academic Journal
- Accession number :
- 21383422
- Full Text :
- https://doi.org/10.1109/TCBB.2011.49