doi: 10.1007/978-1-0716-2609-2_5.
Molecular Dynamics Methods for Antibody Design
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- PMID: 36346588
- DOI: 10.1007/978-1-0716-2609-2_5
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Molecular Dynamics Methods for Antibody Design
Methods Mol Biol.
2023.
Abstract
Complex and coordinated dynamics are closely connected with protein functions, including the binding of antibodies to antigens. Knowledge of such dynamics could improve the design of antibodies. Molecular dynamics (MD) simulations provide a "computational microscope" that can resolve atomic motions and inform antibody design efforts.
Keywords: Antibodies; Molecular dynamics simulation; Protein design; Protein dynamics.
© 2023. Springer Science+Business Media, LLC, part of Springer Nature.
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References
-
- Malito E, Carfi A, Bottomley MJ (2015) Protein crystallography in vaccine research and development. Int J Mol Sci 16:13106–13140. https://doi.org/10.3390/ijms160613106 - DOI - PubMed - PMC
-
- Patrick MH (2007) Crystallography made crystal clear: a guide for users of macromolecular models (3rd Ed.). Biochem Mol Biol Educ 35:387–388. https://doi.org/10.1002/bmb.89 - DOI
-
- Pomés A, Chruszcz M, Gustchina A et al (2015) 100 years later: celebrating the contributions of x-ray crystallography to allergy and clinical immunology. J Allergy Clin Immunol 136:29–37.e10. https://doi.org/10.1016/j.jaci.2015.05.016 - DOI - PubMed - PMC
-
- Berman HM, Battistuz T, Bhat TN et al (2002) The Protein Data Bank. Acta Crystallogr D Biol Crystallogr 58:899–907. https://doi.org/10.1107/s0907444902003451 - DOI - PubMed
-
- Berman HM, Westbrook J, Feng Z et al (2000) The Protein Data Bank. Nucleic Acids Res 28:235–242. https://doi.org/10.1093/nar/28.1.235 - DOI - PubMed - PMC
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