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PIGSPro: prediction of immunoGlobulin structures v2

Rosalba Lepore, Pier P. Olimpieri, Mario A. Messih, Anna Tramontano
2017 Nucleic Acids Research  
PIGSpro is a significant upgrade of the popular PIGS server for the prediction of the structure of immunoglobulins.  ...  ; the selection of the main chain conformation of the hypervariable loops according to the canonical structure model, the prediction of the third loop of the heavy chain (H3) for which complete canonical  ...  structures and to the VH/VL packing.  ... 
doi:10.1093/nar/gkx334 pmid:28472367 pmcid:PMC5570210 fatcat:vwzvoefyf5cshpddavofwyhb5m

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  
Here, we review recent developments in bioinformatics tools for analysis of BCR and TCR repertoires, with an emphasis on those that incorporate structural features.  ...  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.  ...  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

Antibody Lineages with Vaccine-Induced Antigen-Binding Hotspots Develop Broad HIV Neutralization

Rui Kong, Hongying Duan, Zizhang Sheng, Kai Xu, Priyamvada Acharya, Xuejun Chen, Cheng Cheng, Adam S. Dingens, Jason Gorman, Mallika Sastry, Chen-Hsiang Shen, Baoshan Zhang (+44 others)
2019 Cell  
Genetic and structural analyses revealed two of these lineages to belong to a reproducible class capable of neutralizing up to 59% of 208 diverse viral strains.  ...  The vaccine-mediated elicitation of antibodies (Abs) capable of neutralizing diverse HIV-1 strains has been a long-standing goal.  ...  Stuckey forassistance with figures; members of the Electron Microscopy Group at the New York Structural Biology Center (NYSBC) for assistance with data collection; and members of theVirology Laboratory  ... 
doi:10.1016/j.cell.2019.06.030 pmid:31348886 pmcid:PMC6755680 fatcat:as56226nyrhxtc7eziedwb7wzq