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Community-wide assessment of protein-interface modeling suggests improvements to design methodology.
Fleishman SJ, Whitehead TA, Strauch EM, Corn JE, Qin S, Zhou HX, Mitchell JC, Demerdash ON, Takeda-Shitaka M, Terashi G, Moal IH, Li X, Bates PA, Zacharias M, Park H, Ko JS, Lee H, Seok C, Bourquard T, Bernauer J, Poupon A, Azé J, Soner S, Ovali SK, Ozbek P, Tal NB, Haliloglu T, Hwang H, Vreven T, Pierce BG, Weng Z, Pérez-Cano L, Pons C, Fernández-Recio J, Jiang F, Yang F, Gong X, Cao L, Xu X, Liu B, Wang P, Li C, Wang C, Robert CH, Guharoy M, Liu S, Huang Y, Li L, Guo D, Chen Y, Xiao Y, London N, Itzhaki Z, Schueler-Furman O, Inbar Y, Potapov V, Cohen M, Schreiber G, Tsuchiya Y, Kanamori E, Standley DM, Nakamura H, Kinoshita K, Driggers CM, Hall RG, Morgan JL, Hsu VL, Zhan J, Yang Y, Zhou Y, Kastritis PL, Bonvin AM, Zhang W, Camacho CJ, Kilambi KP, Sircar A, Gray JJ, Ohue M, Uchikoga N, Matsuzaki Y, Ishida T, Akiyama Y, Khashan R, Bush S, Fouches D, Tropsha A, Esquivel-Rodríguez J, Kihara D, Stranges PB, Jacak R, Kuhlman B, Huang SY, Zou X, Wodak SJ, Janin J, Baker D. Fleishman SJ, et al. Among authors: yang f, yang y. J Mol Biol. 2011 Nov 25;414(2):289-302. doi: 10.1016/j.jmb.2011.09.031. Epub 2011 Sep 29. J Mol Biol. 2011. PMID: 22001016 Free PMC article.
Crystal structure of the membrane fusion protein CusB from Escherichia coli.
Su CC, Yang F, Long F, Reyon D, Routh MD, Kuo DW, Mokhtari AK, Van Ornam JD, Rabe KL, Hoy JA, Lee YJ, Rajashankar KR, Yu EW. Su CC, et al. Among authors: yang f. J Mol Biol. 2009 Oct 23;393(2):342-55. doi: 10.1016/j.jmb.2009.08.029. Epub 2009 Aug 18. J Mol Biol. 2009. PMID: 19695261 Free PMC article.
Cation-pi interactions at non-redundant protein--RNA interfaces.
Zhang H, Li C, Yang F, Su J, Tan J, Zhang X, Wang C. Zhang H, et al. Among authors: yang f. Biochemistry (Mosc). 2014 Jul;79(7):643-52. doi: 10.1134/S0006297914070062. Biochemistry (Mosc). 2014. PMID: 25108327 Free article.
Conformational change of the AcrR regulator reveals a possible mechanism of induction.
Gu R, Li M, Su CC, Long F, Routh MD, Yang F, McDermott G, Yu EW. Gu R, et al. Among authors: yang f. Acta Crystallogr Sect F Struct Biol Cryst Commun. 2008 Jul 1;64(Pt 7):584-8. doi: 10.1107/S1744309108016035. Epub 2008 Jun 11. Acta Crystallogr Sect F Struct Biol Cryst Commun. 2008. PMID: 18607081 Free PMC article.
DNA looping mediates cooperative transcription activation.
Han SJ, Jiang YL, You LL, Shen LQ, Wu X, Yang F, Cui N, Kong WW, Sun H, Zhou K, Meng HC, Chen ZP, Chen Y, Zhang Y, Zhou CZ. Han SJ, et al. Among authors: yang f. Nat Struct Mol Biol. 2024 Feb;31(2):293-299. doi: 10.1038/s41594-023-01149-7. Epub 2024 Jan 4. Nat Struct Mol Biol. 2024. PMID: 38177666
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