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Items: 1 to 20 of 269

1.

The architecture of the Schizosaccharomyces pombe CCR4-NOT complex.

Ukleja M, Cuellar J, Siwaszek A, Kasprzak JM, Czarnocki-Cieciura M, Bujnicki JM, Dziembowski A, M Valpuesta J.

Nat Commun. 2016 Jan 25;7:10433. doi: 10.1038/ncomms10433.

PMID:
26804377
2.

Loss of conserved non-coding RNAs in genomes of bacterial endosymbionts.

Matelska D, Kurkowska M, Purta E, Bujnicki JM, Dunin-Horkawicz S.

Genome Biol Evol. 2016 Jan 18. pii: evw007. [Epub ahead of print]

3.

Computational modeling of RNA 3D structures and interactions.

Dawson WK, Bujnicki JM.

Curr Opin Struct Biol. 2015 Dec 12;37:22-28. doi: 10.1016/j.sbi.2015.11.007. [Epub ahead of print] Review.

4.

SimRNA: a coarse-grained method for RNA folding simulations and 3D structure prediction.

Boniecki MJ, Lach G, Dawson WK, Tomala K, Lukasz P, Soltysinski T, Rother KM, Bujnicki JM.

Nucleic Acids Res. 2015 Dec 19. pii: gkv1479. [Epub ahead of print]

5.

Structural and functional insights into tRNA binding and adenosine N1-methylation by an archaeal Trm10 homologue.

Van Laer B, Roovers M, Wauters L, Kasprzak JM, Dyzma M, Deyaert E, Kumar Singh R, Feller A, Bujnicki JM, Droogmans L, Versées W.

Nucleic Acids Res. 2016 Jan 29;44(2):940-53. doi: 10.1093/nar/gkv1369. Epub 2015 Dec 15.

6.

Phylogenomics and sequence-structure-function relationships in the GmrSD family of Type IV restriction enzymes.

Machnicka MA, Kaminska KH, Dunin-Horkawicz S, Bujnicki JM.

BMC Bioinformatics. 2015 Oct 23;16:336. doi: 10.1186/s12859-015-0773-z.

7.

Biochemical Characterization and Validation of a Catalytic Site of a Highly Thermostable Ts2631 Endolysin from the Thermus scotoductus Phage vB_Tsc2631.

Plotka M, Kaczorowska AK, Morzywolek A, Makowska J, Kozlowski LP, Thorisdottir A, Skírnisdottir S, Hjörleifsdottir S, Fridjonsson OH, Hreggvidsson GO, Kristjansson JK, Dabrowski S, Bujnicki JM, Kaczorowski T.

PLoS One. 2015 Sep 16;10(9):e0137374. doi: 10.1371/journal.pone.0137374. eCollection 2015.

8.

An atlas of RNA base pairs involving modified nucleobases with optimal geometries and accurate energies.

Chawla M, Oliva R, Bujnicki JM, Cavallo L.

Nucleic Acids Res. 2015 Oct 30;43(19):9573. doi: 10.1093/nar/gkv925. Epub 2015 Sep 10. No abstract available.

9.

Structure and intrinsic disorder of the proteins of the Trypanosoma brucei editosome.

Czerwoniec A, Kasprzak JM, Bytner P, Dobrychłop M, Bujnicki JM.

FEBS Lett. 2015 Sep 14;589(19 Pt A):2603-10. doi: 10.1016/j.febslet.2015.07.026. Epub 2015 Jul 29. Review.

PMID:
26226426
10.

A composite double-/single-stranded RNA-binding region in protein Prp3 supports tri-snRNP stability and splicing.

Liu S, Mozaffari-Jovin S, Wollenhaupt J, Santos KF, Theuser M, Dunin-Horkawicz S, Fabrizio P, Bujnicki JM, Lührmann R, Wahl MC.

Elife. 2015 Jul 10;4:e07320. doi: 10.7554/eLife.07320.

11.

GDFuzz3D: a method for protein 3D structure reconstruction from contact maps, based on a non-Euclidean distance function.

Pietal MJ, Bujnicki JM, Kozlowski LP.

Bioinformatics. 2015 Nov 1;31(21):3499-505. doi: 10.1093/bioinformatics/btv390. Epub 2015 Jun 30.

PMID:
26130575
12.

An atlas of RNA base pairs involving modified nucleobases with optimal geometries and accurate energies.

Chawla M, Oliva R, Bujnicki JM, Cavallo L.

Nucleic Acids Res. 2015 Aug 18;43(14):6714-29. doi: 10.1093/nar/gkv606. Epub 2015 Jun 27. Erratum in: Nucleic Acids Res. 2015 Oct 30;43(19):9573.

13.

The Signature of the Five-Stranded vRRM Fold Defined by Functional, Structural and Computational Analysis of the hnRNP L Protein.

Blatter M, Dunin-Horkawicz S, Grishina I, Maris C, Thore S, Maier T, Bindereif A, Bujnicki JM, Allain FH.

J Mol Biol. 2015 Sep 25;427(19):3001-22. doi: 10.1016/j.jmb.2015.05.020. Epub 2015 Jun 5.

PMID:
26051023
14.

NPDock: a web server for protein-nucleic acid docking.

Tuszynska I, Magnus M, Jonak K, Dawson W, Bujnicki JM.

Nucleic Acids Res. 2015 Jul 1;43(W1):W425-30. doi: 10.1093/nar/gkv493. Epub 2015 May 14.

15.

RNA-Puzzles Round II: assessment of RNA structure prediction programs applied to three large RNA structures.

Miao Z, Adamiak RW, Blanchet MF, Boniecki M, Bujnicki JM, Chen SJ, Cheng C, Chojnowski G, Chou FC, Cordero P, Cruz JA, Ferré-D'Amaré 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.

RNA. 2015 Jun;21(6):1066-84. doi: 10.1261/rna.049502.114. Epub 2015 Apr 16.

16.

Characterization of the termini of the West Nile virus genome and their interactions with the small isoform of the 2' 5'-oligoadenylate synthetase family.

Deo S, Patel TR, Chojnowski G, Koul A, Dzananovic E, McEleney K, Bujnicki JM, McKenna SA.

J Struct Biol. 2015 May;190(2):236-49. doi: 10.1016/j.jsb.2015.04.005. Epub 2015 Apr 11.

PMID:
25871524
17.

Magnesium-binding architectures in RNA crystal structures: validation, binding preferences, classification and motif detection.

Zheng H, Shabalin IG, Handing KB, Bujnicki JM, Minor W.

Nucleic Acids Res. 2015 Apr 20;43(7):3789-801. doi: 10.1093/nar/gkv225. Epub 2015 Mar 23.

18.

Brickworx builds recurrent RNA and DNA structural motifs into medium- and low-resolution electron-density maps.

Chojnowski G, Waleń T, Piątkowski P, Potrzebowski W, Bujnicki JM.

Acta Crystallogr D Biol Crystallogr. 2015 Mar;71(Pt 3):697-705. doi: 10.1107/S1399004715000383. Epub 2015 Feb 26.

19.

Computational methods for prediction of RNA interactions with metal ions and small organic ligands.

Philips A, Łach G, Bujnicki JM.

Methods Enzymol. 2015;553:261-85. doi: 10.1016/bs.mie.2014.10.057. Epub 2015 Feb 3. Review.

PMID:
25726469
20.

Sequence-specific cleavage of dsRNA by Mini-III RNase.

Głów D, Pianka D, Sulej AA, Kozłowski ŁP, Czarnecka J, Chojnowski G, Skowronek KJ, Bujnicki JM.

Nucleic Acids Res. 2015 Mar 11;43(5):2864-73. doi: 10.1093/nar/gkv009. Epub 2015 Jan 29.

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