Journal
IEEE-ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS
Volume 8, Issue 6, Pages 1483-1494Publisher
IEEE COMPUTER SOC
DOI: 10.1109/TCBB.2011.49
Keywords
Epitope prediction; context dependence; antibody; antigen
Categories
Funding
- two Singapore MOE (Ministry Of Education) ARC (Academic Research Council) [T208B2203, MOE2009-T2-2-004]
- Nanyang Technological University [RG66/07]
Ask authors/readers for more resources
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.
Authors
I am an author on this paper
Click your name to claim this paper and add it to your profile.
Reviews
Recommended
No Data Available