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Using 3dRPC for RNA-protein complex structure prediction.
Huang Y, Li H, Xiao Y. Huang Y, et al. Among authors: xiao y. Biophys Rep. 2016;2(5):95-99. doi: 10.1007/s41048-017-0034-y. Epub 2017 Feb 10. Biophys Rep. 2016. PMID: 28317012 Free PMC article.
Preorientation of protein and RNA just before contacting.
Guo D, Liu S, Huang Y, Xiao Y. Guo D, et al. Among authors: xiao y. J Biomol Struct Dyn. 2013;31(7):716-28. doi: 10.1080/07391102.2012.708604. Epub 2012 Aug 22. J Biomol Struct Dyn. 2013. PMID: 22908909
Community-wide evaluation of methods for predicting the effect of mutations on protein-protein interactions.
Moretti R, Fleishman SJ, Agius R, Torchala M, Bates PA, Kastritis PL, Rodrigues JP, Trellet M, Bonvin AM, Cui M, Rooman M, Gillis D, Dehouck Y, Moal I, Romero-Durana M, Perez-Cano L, Pallara C, Jimenez B, Fernandez-Recio J, Flores S, Pacella M, Praneeth Kilambi K, Gray JJ, Popov P, Grudinin S, Esquivel-Rodríguez J, Kihara D, Zhao N, Korkin D, Zhu X, Demerdash ON, Mitchell JC, Kanamori E, Tsuchiya Y, Nakamura H, Lee H, Park H, Seok C, Sarmiento J, Liang S, Teraguchi S, Standley DM, Shimoyama H, Terashi G, Takeda-Shitaka M, Iwadate M, Umeyama H, Beglov D, Hall DR, Kozakov D, Vajda S, Pierce BG, Hwang H, Vreven T, Weng Z, Huang Y, Li H, Yang X, Ji X, Liu S, Xiao Y, Zacharias M, Qin S, Zhou HX, Huang SY, Zou X, Velankar S, Janin J, Wodak SJ, Baker D. Moretti R, et al. Among authors: xiao y. Proteins. 2013 Nov;81(11):1980-7. doi: 10.1002/prot.24356. Epub 2013 Aug 23. Proteins. 2013. PMID: 23843247 Free PMC article.
Advances in RNA 3D Structure Prediction.
Ou X, Zhang Y, Xiong Y, Xiao Y. Ou X, et al. Among authors: xiao y. J Chem Inf Model. 2022 Dec 12;62(23):5862-5874. doi: 10.1021/acs.jcim.2c00939. Epub 2022 Nov 30. J Chem Inf Model. 2022. PMID: 36451090 Review.
RNA-Puzzles Round II: assessment of RNA structure prediction programs applied to three large RNA structures.
Miao Z, Adamiak RW, Blanchet MF, Boniecki M, Bujnicki JM, Chen SJ, Cheng C, Chojnowski G, Chou FC, Cordero P, Cruz JA, Ferré-D'Amaré AR, Das R, Ding F, Dokholyan NV, Dunin-Horkawicz S, Kladwang W, Krokhotin A, Lach G, Magnus M, Major F, Mann TH, Masquida B, Matelska D, Meyer M, Peselis A, Popenda M, Purzycka KJ, Serganov A, Stasiewicz J, Szachniuk M, Tandon A, Tian S, Wang J, Xiao Y, Xu X, Zhang J, Zhao P, Zok T, Westhof E. Miao Z, et al. Among authors: xiao y. RNA. 2015 Jun;21(6):1066-84. doi: 10.1261/rna.049502.114. Epub 2015 Apr 16. RNA. 2015. PMID: 25883046 Free PMC article.
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