Publications

M. Magnus, M. Antczak, T. Zok, J. Wiedemann, P. Lukasiak, Y. Cao, J. M. Bujnicki, E. Westhof, M. Szachniuk, Z. Miao (2020) RNA-Puzzles toolkit: A computational resource of RNA 3D structure benchmark datasets, structure manipulation, and evaluation tools. Nucleic Acids Research, 48(2): 576-588 (doi:10.1093/nar/gkz1108).

Miao Z, Adamiak RW, Antczak M, Boniecki MJ, Bujnicki JM, Chen SJ, Cheng CY, Cheng Y, Chou FC, Das R, Dokholyan NV, Ding F, Geniesse C, Jiang Y, Joshi A, Krokhotin A, Magnus M, Mailhot O, Major F, Mann TH, Piatkowski P, Pluta R, Popenda M, Sarzynska J, Sun L, Szachniuk M, Tian S, Wang J, Watkins AM, Wiedemann J, Xu X, Yesselman JD, Zhang D, Zhang Z, Zhao C, Zhao P, Zhou Y, Zok T, Zyla A, Ren A, Batey RT, Golden BL, Huang L, Lilley DM, Liu Y, Patel DJ, Westhof E (2020) RNA-Puzzles Round IV: 3D structure predictions of four ribozymes and two aptamers. RNA, 26(8): 982-995 (doi:10.1261/rna.075341.120).

Miao Z, Adamiak RW, Antczak M, Batey RT, Becka AJ, Biesiada M, Boniecki MJ, Bujnicki JM, Chen SJ, Cheng CY, Chou FC, Ferre-D'Amare AR, Das R, Dawson WK, Ding F, Dokholyan NV, Dunin-Horkawicz S, Geniesse C, Kappel K, Kladwang W, Krokhotin A, Lach 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 II B, Xiao Y, Xu X, Zhang D, Zok T, Westhof E (2017) RNA-Puzzles Round III: 3D RNA structure prediction of five riboswitches and one ribozyme. RNA, 23(5): 655-672 (doi:10.1261/rna.060368.116).

Miao Z, Adamiak RW, Blanchet MF, Boniecki M, Bujnicki JM, Chen SJ, Cheng C, Chojnowski G, Chou FC, Cordero P, Cruz JA, Ferre-D'Amare 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 (2015) RNA-Puzzles Round II: Assessment of RNA structure prediction programs applied to three large RNA structure. RNA, 21(6): 1066-1084 (doi:10.1261/rna.049502.114).

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 (2012) RNA-Puzzles: a CASP-like evaluation of RNA three-dimensional structure prediction. RNA, 18(4): 610-625 (doi:10.1261/rna.031054.111).