Improved Antibody-Specific Epitope Prediction Using AlphaFold and AbAdapt.

Antibodies recognize their cognate antigens with high affinity and specificity, but the prediction of binding sites on the antigen (epitope) corresponding to a specific antibody remains a challenging problem. To address this problem, we developed AbAdapt, a pipeline that integrates antibody and antigen structural modeling with rigid docking in order to derive antibody-antigen specific features for epitope prediction. In this study, we systematically assessed the impact of integrating the state-of-the-art protein modeling method AlphaFold with the AbAdapt pipeline. By incorporating more accurate antibody models, we observed improvement in docking, paratope prediction, and prediction of antibody-specific epitopes. We further applied AbAdapt-AF in an anti-receptor binding domain (RBD) antibody complex benchmark and found AbAdapt-AF outperformed three alternative docking methods. Also, AbAdapt-AF demonstrated higher epitope prediction accuracy than other tested epitope prediction tools in the anti-RBD antibody complex benchmark. We anticipate that AbAdapt-AF will facilitate prediction of antigen-antibody interactions in a wide range of applications.

Monoclonal Antibodies as Potential Treatment Drugs for Nsp15 and 3CLpro Proteins

Selected monoclonal antibody molecules were conducted using the antibody-antigen docking mode, as well as the antibody-antigen docking approach. The objective of the study was to check the effects of Cetuximab COVID-19 proteins (Nsp15 and 3CLpro) by using antibody-antigen docking mode, as well as the antibody-antigen docking approach. The results of molecular docking revealed that Cetuximab, a cancer-fighting antibody, ranks first among antibodies to both COVID-19 proteins (Nsp15 and 3CLpro). In cetuximab-3CLpro and cetuximab-Nsp15 complexes, the antigen interacts with both antibody chains, H and L. According to the findings, Cetuximab can be added to the COVID-19 treatment protocol, which may have the desired effect of inhibiting viral replication and decreasing mortality by targeting COVID-19 proteins (Nsp15 and 3CLpro). Validation of these computational findings will require additional in vitro and in vivo research, which can be considered as a contribution in the field of biotechnology © 2023, Physical Chemistry Research.All Rights Reserved.