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proABC-2: PRediction Of AntiBody Contacts v2 and its application to information-driven docking [article]

Francesco Ambrosetti, Tobias Hegenlund Olsed, Pier Paolo Olimpieri, Brian Jiménez-García, Edoardo Milanetti, Paolo Marcatilli, Alexandre M.J.J. Bonvin
2020 biorxiv/medrxiv   pre-print
We also demonstrate how the predictions can be fruitfully used to drive the docking in HADDOCK. The proABC-2 server is freely available at: https://bianca.science.uu.nl/proabc2/.  ...  Here we present proABC-2, an update of the original random-forest antibody paratope predictor, based on a convolutional neural network algorithm.  ...  Furthermore, we show how the proABC-2 predictions can be used to drive the modeling of antibody-antigen complexes using the information-driven docking approach HADDOCK (Van Zundert et al., 2016) , which  ... 
doi:10.1101/2020.03.18.967828 fatcat:p3r6vo7fkzatvlhhvl2uyokpdy

Methods for sequence and structural analysis of B and T cell receptor repertoires

Shunsuke Teraguchi, Dianita S. Saputri, Mara Anais Llamas-Covarrubias, Ana Davila, Diego Diez, Sedat Aybars Nazlica, John Rozewicki, Hendra S. Ismanto, Jan Wilamowski, Jiaqi Xie, Zichang Xu, Martin de Jesus Loza-Lopez (+3 others)
2020 Computational and Structural Biotechnology Journal  
We review downstream analyses, including BCR and TCR epitope prediction, antibody-antigen docking and TCR-peptide-MHC Modeling. We also briefly discuss molecular dynamics in this context.  ...  Because the repertoires are highly diverse, specialized software methods are needed to extract meaningful information from BCR and TCR sequence data.  ...  Acknowledgements We would like to thank all members of the Systems Immunology Lab for helpful discussions.  ... 
doi:10.1016/j.csbj.2020.07.008 pmid:32802272 pmcid:PMC7366105 fatcat:6plaw3q47ffbjli7xzxd2v3se4