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Page 1
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: bujnicki jm. Int J Mol Sci. 2022 Aug 25;23(17):9630. doi: 10.3390/ijms23179630. Int J Mol Sci. 2022. PMID: 36077037 Free PMC article.
RNA and protein 3D structure modeling: similarities and differences.
Rother K, Rother M, Boniecki M, Puton T, Bujnicki JM. Rother K, et al. Among authors: bujnicki jm. J Mol Model. 2011 Sep;17(9):2325-36. doi: 10.1007/s00894-010-0951-x. Epub 2011 Jan 22. J Mol Model. 2011. PMID: 21258831 Free PMC article. Review.
ModeRNA: a tool for comparative modeling of RNA 3D structure.
Rother M, Rother K, Puton T, Bujnicki JM. Rother M, et al. Among authors: bujnicki jm. Nucleic Acids Res. 2011 May;39(10):4007-22. doi: 10.1093/nar/gkq1320. Epub 2011 Feb 7. Nucleic Acids Res. 2011. PMID: 21300639 Free PMC article.
Computational methods for prediction of protein-RNA interactions.
Puton T, Kozlowski L, Tuszynska I, Rother K, Bujnicki JM. Puton T, et al. Among authors: bujnicki jm. J Struct Biol. 2012 Sep;179(3):261-8. doi: 10.1016/j.jsb.2011.10.001. Epub 2011 Oct 12. J Struct Biol. 2012. PMID: 22019768 Review.
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. Cruz JA, et al. Among authors: bujnicki jm. RNA. 2012 Apr;18(4):610-25. doi: 10.1261/rna.031054.111. Epub 2012 Feb 23. RNA. 2012. PMID: 22361291 Free PMC article.
RNAlyzer--novel approach for quality analysis of RNA structural models.
Lukasiak P, Antczak M, Ratajczak T, Bujnicki JM, Szachniuk M, Adamiak RW, Popenda M, Blazewicz J. Lukasiak P, et al. Among authors: bujnicki jm. Nucleic Acids Res. 2013 Jul;41(12):5978-90. doi: 10.1093/nar/gkt318. Epub 2013 Apr 25. Nucleic Acids Res. 2013. PMID: 23620294 Free PMC article.
Automated modeling of RNA 3D structure.
Rother K, Rother M, Skiba P, Bujnicki JM. Rother K, et al. Among authors: bujnicki jm. Methods Mol Biol. 2014;1097:395-415. doi: 10.1007/978-1-62703-709-9_18. Methods Mol Biol. 2014. PMID: 24639169 Review.
350 results