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Items: 1 to 20 of 47

1.

SupeRNAlign: a new tool for flexible superposition of homologous RNA structures and inference of accurate structure-based sequence alignments.

Piatkowski P, Jablonska J, Zyla A, Niedzialek D, Matelska D, Jankowska E, Walen T, Dawson WK, Bujnicki JM.

Nucleic Acids Res. 2017 Sep 19;45(16):e150. doi: 10.1093/nar/gkx631.

PMID:
28934487
2.

Mutations in human AID differentially affect its ability to deaminate cytidine and 5-methylcytidine in ssDNA substrates in vitro.

Budzko L, Jackowiak P, Kamel K, Sarzynska J, Bujnicki JM, Figlerowicz M.

Sci Rep. 2017 Jun 20;7(1):3873. doi: 10.1038/s41598-017-03936-x.

3.

Defining the crucial domain and amino acid residues in bacterial Lon protease for DNA binding and processing of DNA-interacting substrates.

Karlowicz A, Wegrzyn K, Gross M, Kaczynska D, Ropelewska M, Siemiątkowska M, Bujnicki JM, Konieczny I.

J Biol Chem. 2017 May 5;292(18):7507-7518. doi: 10.1074/jbc.M116.766709. Epub 2017 Mar 14.

PMID:
28292931
4.

RNA-Puzzles Round III: 3D RNA structure prediction of five riboswitches and one ribozyme.

Miao Z, Adamiak RW, Antczak M, Batey RT, Becka AJ, Biesiada M, Boniecki MJ, Bujnicki JM, Chen SJ, Cheng CY, Chou FC, Ferré-D'Amaré AR, Das R, Dawson WK, Ding F, Dokholyan NV, Dunin-Horkawicz S, Geniesse C, Kappel K, Kladwang W, Krokhotin A, Łach GE, Major F, Mann TH, Magnus M, Pachulska-Wieczorek K, Patel DJ, Piccirilli JA, Popenda M, Purzycka KJ, Ren A, Rice GM, Santalucia J Jr, Sarzynska J, Szachniuk M, Tandon A, Trausch JJ, Tian S, Wang J, Weeks KM, Williams B 2nd, Xiao Y, Xu X, Zhang D, Zok T, Westhof E.

RNA. 2017 May;23(5):655-672. doi: 10.1261/rna.060368.116. Epub 2017 Jan 30.

5.

Structural studies of RNA-protein complexes: A hybrid approach involving hydrodynamics, scattering, and computational methods.

Patel TR, Chojnowski G, Astha, Koul A, McKenna SA, Bujnicki JM.

Methods. 2017 Apr 15;118-119:146-162. doi: 10.1016/j.ymeth.2016.12.002. Epub 2016 Dec 8. Review.

6.

RNA 3D Structure Modeling by Combination of Template-Based Method ModeRNA, Template-Free Folding with SimRNA, and Refinement with QRNAS.

Piatkowski P, Kasprzak JM, Kumar D, Magnus M, Chojnowski G, Bujnicki JM.

Methods Mol Biol. 2016;1490:217-35. doi: 10.1007/978-1-4939-6433-8_14.

PMID:
27665602
7.

Coarse-grained modeling of RNA 3D structure.

Dawson WK, Maciejczyk M, Jankowska EJ, Bujnicki JM.

Methods. 2016 Jul 1;103:138-56. doi: 10.1016/j.ymeth.2016.04.026. Epub 2016 Apr 25. Review.

8.

SimRNAweb: a web server for RNA 3D structure modeling with optional restraints.

Magnus M, Boniecki MJ, Dawson W, Bujnicki JM.

Nucleic Acids Res. 2016 Jul 8;44(W1):W315-9. doi: 10.1093/nar/gkw279. Epub 2016 Apr 19.

9.

Modeling of Protein-RNA Complex Structures Using Computational Docking Methods.

Madan B, Kasprzak JM, Tuszynska I, Magnus M, Szczepaniak K, Dawson WK, Bujnicki JM.

Methods Mol Biol. 2016;1414:353-72. doi: 10.1007/978-1-4939-3569-7_21.

PMID:
27094302
10.

tRNAmodpred: A computational method for predicting posttranscriptional modifications in tRNAs.

Machnicka MA, Dunin-Horkawicz S, de Crécy-Lagard V, Bujnicki JM.

Methods. 2016 Sep 1;107:34-41. doi: 10.1016/j.ymeth.2016.03.013. Epub 2016 Mar 23.

11.

The architecture of the Schizosaccharomyces pombe CCR4-NOT complex.

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

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

12.

Loss of Conserved Noncoding RNAs in Genomes of Bacterial Endosymbionts.

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

Genome Biol Evol. 2016 Jan 18;8(2):426-38. doi: 10.1093/gbe/evw007.

13.

Computational modeling of RNA 3D structures and interactions.

Dawson WK, Bujnicki JM.

Curr Opin Struct Biol. 2016 Apr;37:22-8. doi: 10.1016/j.sbi.2015.11.007. Epub 2015 Dec 12. Review.

14.

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.

15.

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.

16.

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.

17.

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.

18.

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
19.

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.

20.

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

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