Publication

Publications from the RNA-Puzzles community can be found on (pubmed).

  • RNA-Puzzles toolkit: a computational resource of RNA 3D structure benchmark datasets, structure manipulation, and evaluation tools. Magnus, M., Antczak, M., Zok, T., Wiedemann, J., Lukasiak, P., Cao, Y., Bujnicki, J. M., Westhof, E., Szachniuk, M. & Miao, Z.# Nucleic Acids Res. 48, 576–588 (2020).

  • Evaluation of the stereochemical quality of predicted RNA 3D models in the RNA-Puzzles submissions. Carrascoza, F., Antczak, M., Miao, Z.#, Westhof, E. & Szachniuk, M.# RNA (2021). doi:10.1261/rna.078685.121.

  • Advances in RNA 3D Structure Modeling Using Experimental Data. Li, B., Cao, Y., Westhof, E. & Miao, Z.# Front. Genet. 11:574485, (2020).

  • RNA Structure: Advances and Assessment of 3D Structure Prediction. Miao, Z.# & Westhof, E.# Annu. Rev. Biophys. 46, 483–503 (2017).

  • RNA-Puzzles Round IV: 3D structure predictions of four ribozymes and two aptamers. Miao, Z., Adamiak, R. W., Antczak, M., Boniecki, M. J., Bujnicki, J., Chen, S.-J., Cheng, C. Y., Cheng, Y., Chou, F.-C., Das, R., Dokholyan, N. V., Ding, F., Geniesse, C., Jiang, Y., Joshi, A., Krokhotin, A., Magnus, M., Mailhot, O., Major, F., Mann, T. H., Piątkowski, P., Pluta, R., Popenda, M., Sarzynska, J., Sun, L., Szachniuk, M., Tian, S., Wang, J., Wang, J., Watkins, A. M., Wiedemann, J., Xiao, Y., Xu, X., Yesselman, J. D., Zhang, D., Zhang, Y., Zhang, Z., Zhao, C., Zhao, P., Zhou, Y., Zok, T., Żyła, A., Ren, A., Batey, R. T., Golden, B. L., Huang, L., Lilley, D. M., Liu, Y., Patel, D. J. & Westhof, E.# RNA 26, 982–995 (2020).

  • RNA-Puzzles Round III: 3D RNA structure prediction of five riboswitches and one ribozyme. Miao Z, Adamiak RW, Antczak M, Batey RT, Becka AJ, Biesiada M, Boniecki MJ, Bujnicki JM, Chen SJ, Cheng CY, Chou FC, Ferré-D'Amaré AR, Das R, Dawson WK, Ding F, Dokholyan NV, Dunin-Horkawicz S, Geniesse C, Kappel K, Kladwang W, Krokhotin A, Łach GE, Major F, Mann TH, Magnus M, Pachulska-Wieczorek K, Patel DJ, Piccirilli JA, Popenda M, Purzycka KJ, Ren A, Rice GM, Santalucia J Jr, Sarzynska J, Szachniuk M, Tandon A, Trausch JJ, Tian S, Wang J, Weeks KM, Williams B 2nd, Xiao Y, Xu X, Zhang D, Zok T, Westhof E. RNA. 2017 May;23(5):655-672. doi: 10.1261/rna.060368.116. Epub 2017 Jan 30.

  • 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. RNA. 2015 Jun;21(6):1066-84. doi: 10.1261/rna.049502.114. Epub 2015 Apr 16. PMID: 25883046 Free PMC Article

  • RNA-Puzzles: a CASP-like evaluation of RNA three-dimensional structure prediction. Cruz JA, Blanchet MF, Boniecki M, Bujnicki JM, Chen SJ, Cao S, Das R, Ding F, Dokholyan NV, Flores SC, Huang L, Lavender CA, Lisi V, Major F, Mikolajczak K, Patel DJ, Philips A, Puton T, Santalucia J, Sijenyi F, Hermann T, Rother K, Rother M, Serganov A, Skorupski M, Soltysinski T, Sripakdeevong P, Tuszynska I, Weeks KM, Waldsich C, Wildauer M, Leontis NB, Westhof E. RNA. 2012 Apr;18(4):610-25. doi: 10.1261/rna.031054.111. Epub 2012 Feb 23. PMID: 22361291 Free PMC Article