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Page 1
RNA-Puzzles Round V: blind predictions of 23 RNA structures.
Bu F, Adam Y, Adamiak RW, Antczak M, de Aquino BRH, Badepally NG, Batey RT, Baulin EF, Boinski P, Boniecki MJ, Bujnicki JM, Carpenter KA, Chacon J, Chen SJ, Chiu W, Cordero P, Das NK, Das R, Dawson WK, DiMaio F, Ding F, Dock-Bregeon AC, Dokholyan NV, Dror RO, Dunin-Horkawicz S, Eismann S, Ennifar E, Esmaeeli R, Farsani MA, Ferré-D'Amaré AR, Geniesse C, Ghanim GE, Guzman HV, Hood IV, Huang L, Jain DS, Jaryani F, Jin L, Joshi A, Karelina M, Kieft JS, Kladwang W, Kmiecik S, Koirala D, Kollmann M, Kretsch RC, Kurciński M, Li J, Li S, Magnus M, Masquida B, Moafinejad SN, Mondal A, Mukherjee S, Nguyen THD, Nikolaev G, Nithin C, Nye G, Pandaranadar Jeyeram IPN, Perez A, Pham P, Piccirilli JA, Pilla SP, Pluta R, Poblete S, Ponce-Salvatierra A, Popenda M, Popenda L, Pucci F, Rangan R, Ray A, Ren A, Sarzynska J, Sha CM, Stefaniak F, Su Z, Suddala KC, Szachniuk M, Townshend R, Trachman RJ 3rd, Wang J, Wang W, Watkins A, Wirecki TK, Xiao Y, Xiong P, Xiong Y, Yang J, Yesselman JD, Zhang J, Zhang Y, Zhang Z, Zhou Y, Zok T, Zhang D, Zhang S, Żyła A, Westhof E, Miao Z. Bu F, et al. Among authors: zok t. Nat Methods. 2024 Dec 2. doi: 10.1038/s41592-024-02543-9. Online ahead of print. Nat Methods. 2024. PMID: 39623050 Free article.
Datasets for Benchmarking RNA Design Algorithms.
Badura J, Zok T, Rybarczyk A. Badura J, et al. Among authors: zok t. Methods Mol Biol. 2025;2847:229-240. doi: 10.1007/978-1-0716-4079-1_16. Methods Mol Biol. 2025. PMID: 39312148
Knotted artifacts in predicted 3D RNA structures.
Gren BA, Antczak M, Zok T, Sulkowska JI, Szachniuk M. Gren BA, et al. Among authors: zok t. PLoS Comput Biol. 2024 Jun 20;20(6):e1011959. doi: 10.1371/journal.pcbi.1011959. eCollection 2024 Jun. PLoS Comput Biol. 2024. PMID: 38900780 Free PMC article.
When will RNA get its AlphaFold moment?
Schneider B, Sweeney BA, Bateman A, Cerny J, Zok T, Szachniuk M. Schneider B, et al. Among authors: zok t. Nucleic Acids Res. 2023 Oct 13;51(18):9522-9532. doi: 10.1093/nar/gkad726. Nucleic Acids Res. 2023. PMID: 37702120 Free PMC article.
New prediction categories in CASP15.
Kryshtafovych A, Antczak M, Szachniuk M, Zok T, Kretsch RC, Rangan R, Pham P, Das R, Robin X, Studer G, Durairaj J, Eberhardt J, Sweeney A, Topf M, Schwede T, Fidelis K, Moult J. Kryshtafovych A, et al. Among authors: zok t. Proteins. 2023 Dec;91(12):1550-1557. doi: 10.1002/prot.26515. Epub 2023 Jun 12. Proteins. 2023. PMID: 37306011 Free PMC article.
Computational Pipeline for Reference-Free Comparative Analysis of RNA 3D Structures Applied to SARS-CoV-2 UTR Models.
Gumna J, Antczak M, Adamiak RW, Bujnicki JM, Chen SJ, Ding F, Ghosh P, Li J, Mukherjee S, Nithin C, Pachulska-Wieczorek K, Ponce-Salvatierra A, Popenda M, Sarzynska J, Wirecki T, Zhang D, Zhang S, Zok T, Westhof E, Miao Z, Szachniuk M, Rybarczyk A. Gumna J, et al. Among authors: zok t. Int J Mol Sci. 2022 Aug 25;23(17):9630. doi: 10.3390/ijms23179630. Int J Mol Sci. 2022. PMID: 36077037 Free PMC article.
RNAloops: a database of RNA multiloops.
Wiedemann J, Kaczor J, Milostan M, Zok T, Blazewicz J, Szachniuk M, Antczak M. Wiedemann J, et al. Among authors: zok t. Bioinformatics. 2022 Sep 2;38(17):4200-4205. doi: 10.1093/bioinformatics/btac484. Bioinformatics. 2022. PMID: 35809063 Free PMC article.
Characterizing domain-specific open educational resources by linking ISCB Communities of Special Interest to Wikipedia.
Kilpatrick AM, Rahman F, Anjum A, Shome S, Andalib KMS, Banik S, Chowdhury SF, Coombe P, Astroz YC, Douglas JM, Eranti P, Kiran AD, Kumar S, Lim H, Lorenzi V, Lubiana T, Mahmud S, Puche R, Rybarczyk A, Al Sium SM, Twesigomwe D, Zok T, Orengo CA, Friedberg I, Kelso JF, Welch L. Kilpatrick AM, et al. Among authors: zok t. Bioinformatics. 2022 Jun 24;38(Suppl 1):i19-i27. doi: 10.1093/bioinformatics/btac236. Bioinformatics. 2022. PMID: 35758800 Free PMC article.
30 results