CSDL Home IEEE/ACM Transactions on Computational Biology and Bioinformatics 2011 vol.8 Issue No.06 - November/December
Issue No.06 - November/December (2011 vol.8)
Liang Zhao , Bioinf. Res. Center, Nanyang Technol. Univ., Singapore, Singapore
Jinyan Li , Sch. of Comput., Nat. Univ. of Singapore, Singapore, Singapore
DOI Bookmark: http://doi.ieeecomputersociety.org/10.1109/TCBB.2011.49
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.
proteins, association, biochemistry, bioinformatics, cellular biophysics, classification, Markov processes, molecular biophysics, molecular configurations, prediction theory, nonredundant data set, antibody-specified B-cell epitope prediction, context awareness, antigen recognition, antibody recognition, epitope residues reconfiguration, coarse binary classification, association, residues-residues pairing preference, contact residue pairs, interacting paratope-epitope residues, relative composition, cooperativity ratios, Markov properties, Hidden Markov models, Context awareness, Bioinformatics, Computational biology, Green products, antigen., Epitope prediction, context dependence, antibody
Liang Zhao, Jinyan Li, "Antibody-Specified B-Cell Epitope Prediction in Line with the Principle of Context-Awareness", IEEE/ACM Transactions on Computational Biology and Bioinformatics, vol.8, no. 6, pp. 1483-1494, November/December 2011, doi:10.1109/TCBB.2011.49