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Cryo-EM Structures Delineate a pH-Dependent Switch that Mediates Endosomal Positioning of SARS-CoV-2 Spike Receptor-Binding Domains.
Zhou T, Tsybovsky Y, Olia AS, Gorman J, Rapp MA, Cerutti G, Chuang GY, Katsamba PS, Nazzari A, Sampson JM, Schon A, Wang PD, Bimela J, Shi W, Teng IT, Zhang B, Boyington JC, Sastry M, Stephens T, Stuckey J, Wang S, Friesner RA, Ho DD, Mascola JR, Shapiro L, Kwong PD. Zhou T, et al. Among authors: friesner ra. bioRxiv [Preprint]. 2020 Jul 31:2020.07.04.187989. doi: 10.1101/2020.07.04.187989. bioRxiv. 2020. Update in: Cell Host Microbe. 2020 Dec 9;28(6):867-879.e5. doi: 10.1016/j.chom.2020.11.004. PMID: 32637958 Free PMC article. Updated. Preprint.
Free Energy Perturbation Calculation of Relative Binding Free Energy between Broadly Neutralizing Antibodies and the gp120 Glycoprotein of HIV-1.
Clark AJ, Gindin T, Zhang B, Wang L, Abel R, Murret CS, Xu F, Bao A, Lu NJ, Zhou T, Kwong PD, Shapiro L, Honig B, Friesner RA. Clark AJ, et al. Among authors: friesner ra. J Mol Biol. 2017 Apr 7;429(7):930-947. doi: 10.1016/j.jmb.2016.11.021. Epub 2016 Nov 28. J Mol Biol. 2017. PMID: 27908641 Free PMC article.
Cryo-EM Structures of SARS-CoV-2 Spike without and with ACE2 Reveal a pH-Dependent Switch to Mediate Endosomal Positioning of Receptor-Binding Domains.
Zhou T, Tsybovsky Y, Gorman J, Rapp M, Cerutti G, Chuang GY, Katsamba PS, Sampson JM, Schön A, Bimela J, Boyington JC, Nazzari A, Olia AS, Shi W, Sastry M, Stephens T, Stuckey J, Teng IT, Wang P, Wang S, Zhang B, Friesner RA, Ho DD, Mascola JR, Shapiro L, Kwong PD. Zhou T, et al. Among authors: friesner ra. Cell Host Microbe. 2020 Dec 9;28(6):867-879.e5. doi: 10.1016/j.chom.2020.11.004. Epub 2020 Nov 17. Cell Host Microbe. 2020. PMID: 33271067 Free PMC article.
Robust prediction of relative binding energies for protein-protein complex mutations using free energy perturbation calculations.
Sampson JM, Cannon DA, Duan J, Epstein JCK, Sergeeva AP, Katsamba PS, Mannepalli SM, Bahna FA, Adihou H, Guéret SM, Gopalakrishnan R, Geschwindner S, Rees DG, Sigurdardottir A, Wilkinson T, Dodd RB, De Maria L, Mobarec JC, Shapiro L, Honig B, Buchanan A, Friesner RA, Wang L. Sampson JM, et al. Among authors: friesner ra. bioRxiv [Preprint]. 2024 Apr 24:2024.04.22.590325. doi: 10.1101/2024.04.22.590325. bioRxiv. 2024. PMID: 38712280 Free PMC article. Preprint.
A hierarchical approach to all-atom protein loop prediction.
Jacobson MP, Pincus DL, Rapp CS, Day TJ, Honig B, Shaw DE, Friesner RA. Jacobson MP, et al. Among authors: friesner ra. Proteins. 2004 May 1;55(2):351-67. doi: 10.1002/prot.10613. Proteins. 2004. PMID: 15048827
206 results