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Antibody-Specified B-Cell Epitope Prediction in Line with the Principle of Context-Awareness
November/December 2011 (vol. 8 no. 6)
pp. 1483-1494
Liang Zhao, Bioinf. Res. Center, Nanyang Technol. Univ., Singapore, Singapore
Limsoon Wong, Sch. of Comput., Nat. Univ. of Singapore, Singapore, Singapore
Jinyan Li, Sch. of Comput., Nat. Univ. of Singapore, Singapore, Singapore
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.

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Index Terms:
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, Limsoon Wong, 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, Nov.-Dec. 2011, doi:10.1109/TCBB.2011.49
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