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MODOMICS: a database of RNA modification pathways. 2017 update.
Boccaletto P, Machnicka MA, Purta E, Piatkowski P, Baginski B, Wirecki TK, de Crécy-Lagard V, Ross R, Limbach PA, Kotter A, Helm M, Bujnicki JM. Boccaletto P, et al. Among authors: wirecki tk. Nucleic Acids Res. 2018 Jan 4;46(D1):D303-D307. doi: 10.1093/nar/gkx1030. Nucleic Acids Res. 2018. PMID: 29106616 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. Int J Mol Sci. 2022 Aug 25;23(17):9630. doi: 10.3390/ijms23179630. Int J Mol Sci. 2022. PMID: 36077037 Free PMC article.
SimRNAweb v2.0: a web server for RNA folding simulations and 3D structure modeling, with optional restraints and enhanced analysis of folding trajectories.
Moafinejad SN, de Aquino BRH, Boniecki MJ, Pandaranadar Jeyeram IPN, Nikolaev G, Magnus M, Farsani MA, Badepally NG, Wirecki TK, Stefaniak F, Bujnicki JM. Moafinejad SN, et al. Among authors: wirecki tk. Nucleic Acids Res. 2024 Jul 5;52(W1):W368-W373. doi: 10.1093/nar/gkae356. Nucleic Acids Res. 2024. PMID: 38738621 Free PMC article.
A unified coarse-grained model of biological macromolecules based on mean-field multipole-multipole interactions.
Liwo A, Baranowski M, Czaplewski C, Gołaś E, He Y, Jagieła D, Krupa P, Maciejczyk M, Makowski M, Mozolewska MA, Niadzvedtski A, Ołdziej S, Scheraga HA, Sieradzan AK, Slusarz R, Wirecki T, Yin Y, Zaborowski B. Liwo A, et al. J Mol Model. 2014 Aug;20(8):2306. doi: 10.1007/s00894-014-2306-5. Epub 2014 Jul 15. J Mol Model. 2014. PMID: 25024008 Free PMC article.
15 results