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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: puton t. 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: puton t. 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.
ModeRNA server: an online tool for modeling RNA 3D structures.
Rother M, Milanowska K, Puton T, Jeleniewicz J, Rother K, Bujnicki JM. Rother M, et al. Among authors: puton t. Bioinformatics. 2011 Sep 1;27(17):2441-2. doi: 10.1093/bioinformatics/btr400. Epub 2011 Jul 4. Bioinformatics. 2011. PMID: 21727140
RNA tertiary structure prediction with ModeRNA.
Rother M, Rother K, Puton T, Bujnicki JM. Rother M, et al. Among authors: puton t. Brief Bioinform. 2011 Nov;12(6):601-13. doi: 10.1093/bib/bbr050. Epub 2011 Sep 6. Brief Bioinform. 2011. PMID: 21896613
A toolbox for developing bioinformatics software.
Rother K, Potrzebowski W, Puton T, Rother M, Wywial E, Bujnicki JM. Rother K, et al. Among authors: puton t. Brief Bioinform. 2012 Mar;13(2):244-57. doi: 10.1093/bib/bbr035. Epub 2011 Jul 29. Brief Bioinform. 2012. PMID: 21803787 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. Cruz JA, et al. Among authors: puton t. RNA. 2012 Apr;18(4):610-25. doi: 10.1261/rna.031054.111. Epub 2012 Feb 23. RNA. 2012. PMID: 22361291 Free PMC article.