SnugDock: Paratope Structural Optimization during Antibody-Antigen Docking Compensates for Errors in Antibody Homology Models
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Abstract
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DOI: 10.1371/journal.pcbi.1000644
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References listed on IDEAS
- Grant E. Nybakken & Theodore Oliphant & Syd Johnson & Stephen Burke & Michael S. Diamond & Daved H. Fremont, 2005. "Structural basis of West Nile virus neutralization by a therapeutic antibody," Nature, Nature, vol. 437(7059), pages 764-769, September.
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- Thillai V. Sekar & Eslam A. Elghonaimy & Katy L. Swancutt & Sebastian Diegeler & Isaac Gonzalez & Cassandra Hamilton & Peter Q. Leung & Jens Meiler & Cristina E. Martina & Michael Whitney & Todd A. Ag, 2023. "Simultaneous selection of nanobodies for accessible epitopes on immune cells in the tumor microenvironment," Nature Communications, Nature, vol. 14(1), pages 1-20, December.
- Massih Khorvash & Nick Blinov & Carol Ladner-Keay & Jie Lu & Judith M Silverman & Ebrima Gibbs & Yu Tian Wang & Andriy Kovalenko & David Wishart & Neil R Cashman, 2020. "Molecular interactions between monoclonal oligomer-specific antibody 5E3 and its amyloid beta cognates," PLOS ONE, Public Library of Science, vol. 15(5), pages 1-35, May.
- Jordan R Willis & Bryan S Briney & Samuel L DeLuca & James E Crowe Jr & Jens Meiler, 2013. "Human Germline Antibody Gene Segments Encode Polyspecific Antibodies," PLOS Computational Biology, Public Library of Science, vol. 9(4), pages 1-14, April.
- Haohuai He & Bing He & Lei Guan & Yu Zhao & Feng Jiang & Guanxing Chen & Qingge Zhu & Calvin Yu-Chian Chen & Ting Li & Jianhua Yao, 2024. "De novo generation of SARS-CoV-2 antibody CDRH3 with a pre-trained generative large language model," Nature Communications, Nature, vol. 15(1), pages 1-19, December.
- Jeffrey A. Ruffolo & Lee-Shin Chu & Sai Pooja Mahajan & Jeffrey J. Gray, 2023. "Fast, accurate antibody structure prediction from deep learning on massive set of natural antibodies," Nature Communications, Nature, vol. 14(1), pages 1-13, December.
- Julia Koehler Leman & Sergey Lyskov & Steven M. Lewis & Jared Adolf-Bryfogle & Rebecca F. Alford & Kyle Barlow & Ziv Ben-Aharon & Daniel Farrell & Jason Fell & William A. Hansen & Ameya Harmalkar & Je, 2021. "Ensuring scientific reproducibility in bio-macromolecular modeling via extensive, automated benchmarks," Nature Communications, Nature, vol. 12(1), pages 1-15, December.
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