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Results: 1 to 20 of 24

1.

Computational modeling of RNA 3D structures, with the aid of experimental restraints.

Magnus M, Matelska D, Lach G, Chojnowski G, Boniecki MJ, Purta E, Dawson W, Dunin-Horkawicz S, Bujnicki JM.

RNA Biol. 2014 Apr 23;11(5). pii: 28826. Epub 2014 Apr 23. Review.

PMID:
24785264
[PubMed - as supplied by publisher]
Free Article
2.

Solution conformation of adenovirus virus associated RNA-I and its interaction with PKR.

Dzananovic E, Patel TR, Chojnowski G, Boniecki MJ, Deo S, McEleney K, Harding SE, Bujnicki JM, McKenna SA.

J Struct Biol. 2014 Jan;185(1):48-57. doi: 10.1016/j.jsb.2013.11.007. Epub 2013 Nov 28.

PMID:
24291322
[PubMed - indexed for MEDLINE]
3.

S6:S18 ribosomal protein complex interacts with a structural motif present in its own mRNA.

Matelska D, Purta E, Panek S, Boniecki MJ, Bujnicki JM, Dunin-Horkawicz S.

RNA. 2013 Oct;19(10):1341-8. doi: 10.1261/rna.038794.113. Epub 2013 Aug 26.

PMID:
23980204
[PubMed - indexed for MEDLINE]
4.

Leucyl-tRNA synthetase editing domain functions as a molecular rheostat to control codon ambiguity in Mycoplasma pathogens.

Li L, Palencia A, Lukk T, Li Z, Luthey-Schulten ZA, Cusack S, Martinis SA, Boniecki MT.

Proc Natl Acad Sci U S A. 2013 Mar 5;110(10):3817-22. doi: 10.1073/pnas.1218374110. Epub 2013 Feb 19.

PMID:
23431144
[PubMed - indexed for MEDLINE]
Free PMC Article
5.

Rational engineering of sequence specificity in R.MwoI restriction endonuclease.

Skowronek K, Boniecki MJ, Kluge B, Bujnicki JM.

Nucleic Acids Res. 2012 Sep 1;40(17):8579-92. Epub 2012 Jun 25.

PMID:
22735699
[PubMed - indexed for MEDLINE]
Free PMC Article
6.

Yeast mitochondrial leucyl-tRNA synthetase CP1 domain has functionally diverged to accommodate RNA splicing at expense of hydrolytic editing.

Sarkar J, Poruri K, Boniecki MT, McTavish KK, Martinis SA.

J Biol Chem. 2012 Apr 27;287(18):14772-81. doi: 10.1074/jbc.M111.322412. Epub 2012 Mar 1.

PMID:
22383526
[PubMed - indexed for MEDLINE]
Free PMC Article
7.

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.

RNA. 2012 Apr;18(4):610-25. doi: 10.1261/rna.031054.111. Epub 2012 Feb 23.

PMID:
22361291
[PubMed - indexed for MEDLINE]
Free PMC Article
8.

Coordination of tRNA synthetase active sites for chemical fidelity.

Boniecki MT, Martinis SA.

J Biol Chem. 2012 Mar 30;287(14):11285-9. doi: 10.1074/jbc.C111.325795. Epub 2012 Feb 13.

PMID:
22334703
[PubMed - indexed for MEDLINE]
Free PMC Article
9.

MetalionRNA: computational predictor of metal-binding sites in RNA structures.

Philips A, Milanowska K, Lach G, Boniecki M, Rother K, Bujnicki JM.

Bioinformatics. 2012 Jan 15;28(2):198-205. doi: 10.1093/bioinformatics/btr636. Epub 2011 Nov 21.

PMID:
22110243
[PubMed - indexed for MEDLINE]
Free PMC Article
10.

Naturally occurring aminoacyl-tRNA synthetases editing-domain mutations that cause mistranslation in Mycoplasma parasites.

Li L, Boniecki MT, Jaffe JD, Imai BS, Yau PM, Luthey-Schulten ZA, Martinis SA.

Proc Natl Acad Sci U S A. 2011 Jun 7;108(23):9378-83. doi: 10.1073/pnas.1016460108. Epub 2011 May 23.

PMID:
21606343
[PubMed - indexed for MEDLINE]
Free PMC Article
11.

RNA and protein 3D structure modeling: similarities and differences.

Rother K, Rother M, Boniecki M, Puton T, Bujnicki JM.

J Mol Model. 2011 Sep;17(9):2325-36. doi: 10.1007/s00894-010-0951-x. Epub 2011 Jan 22. Review.

PMID:
21258831
[PubMed - indexed for MEDLINE]
Free PMC Article
12.

The balance between pre- and post-transfer editing in tRNA synthetases.

Martinis SA, Boniecki MT.

FEBS Lett. 2010 Jan 21;584(2):455-9. doi: 10.1016/j.febslet.2009.11.071. Epub . Review.

PMID:
19941860
[PubMed - indexed for MEDLINE]
Free PMC Article
13.

Leucyl-tRNA synthetase-dependent and -independent activation of a group I intron.

Boniecki MT, Rho SB, Tukalo M, Hsu JL, Romero EP, Martinis SA.

J Biol Chem. 2009 Sep 25;284(39):26243-50. doi: 10.1074/jbc.M109.031179. Epub 2009 Jul 21.

PMID:
19622748
[PubMed - indexed for MEDLINE]
Free PMC Article
14.

CP1-dependent partitioning of pretransfer and posttransfer editing in leucyl-tRNA synthetase.

Boniecki MT, Vu MT, Betha AK, Martinis SA.

Proc Natl Acad Sci U S A. 2008 Dec 9;105(49):19223-8. doi: 10.1073/pnas.0809336105. Epub 2008 Nov 19.

PMID:
19020078
[PubMed - indexed for MEDLINE]
Free PMC Article
15.

Type II restriction endonuclease R.Hpy188I belongs to the GIY-YIG nuclease superfamily, but exhibits an unusual active site.

Kaminska KH, Kawai M, Boniecki M, Kobayashi I, Bujnicki JM.

BMC Struct Biol. 2008 Nov 14;8:48. doi: 10.1186/1472-6807-8-48.

PMID:
19014591
[PubMed - indexed for MEDLINE]
Free PMC Article
16.

In vitro assays for the determination of aminoacyl-tRNA synthetase editing activity.

Splan KE, Musier-Forsyth K, Boniecki MT, Martinis SA.

Methods. 2008 Feb;44(2):119-28. doi: 10.1016/j.ymeth.2007.10.009.

PMID:
18241793
[PubMed - indexed for MEDLINE]
Free PMC Article
17.

Structural bioinformatics analysis of enzymes involved in the biosynthesis pathway of the hypermodified nucleoside ms(2)io(6)A37 in tRNA.

Kaminska KH, Baraniak U, Boniecki M, Nowaczyk K, Czerwoniec A, Bujnicki JM.

Proteins. 2008 Jan 1;70(1):1-18.

PMID:
17910062
[PubMed - indexed for MEDLINE]
18.

I-Ssp6803I: the first homing endonuclease from the PD-(D/E)XK superfamily exhibits an unusual mode of DNA recognition.

Orlowski J, Boniecki M, Bujnicki JM.

Bioinformatics. 2007 Mar 1;23(5):527-30. Epub 2007 Jan 22.

PMID:
17242028
[PubMed - indexed for MEDLINE]
Free Article
19.

A viable amino acid editing activity in the leucyl-tRNA synthetase CP1-splicing domain is not required in the yeast mitochondria.

Karkhanis VA, Boniecki MT, Poruri K, Martinis SA.

J Biol Chem. 2006 Nov 3;281(44):33217-25. Epub 2006 Sep 6.

PMID:
16956879
[PubMed - indexed for MEDLINE]
Free Article
20.

FRankenstein becomes a cyborg: the automatic recombination and realignment of fold recognition models in CASP6.

Kosinski J, Gajda MJ, Cymerman IA, Kurowski MA, Pawlowski M, Boniecki M, Obarska A, Papaj G, Sroczynska-Obuchowicz P, Tkaczuk KL, Sniezynska P, Sasin JM, Augustyn A, Bujnicki JM, Feder M.

Proteins. 2005;61 Suppl 7:106-13.

PMID:
16187351
[PubMed - indexed for MEDLINE]

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