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Items: 28

1.

Anti-Resonant Hollow Core Fibers with Modified Shape of the Core for the Better Optical Performance in the Visible Spectral Region-A Numerical Study.

Stawska HI, Popenda MA, Bereś-Pawlik E.

Polymers (Basel). 2018 Aug 10;10(8). pii: E899. doi: 10.3390/polym10080899.

2.

RNAfitme: a webserver for modeling nucleobase and nucleoside residue conformation in fixed-backbone RNA structures.

Antczak M, Zok T, Osowiecki M, Popenda M, Adamiak RW, Szachniuk M.

BMC Bioinformatics. 2018 Aug 22;19(1):304. doi: 10.1186/s12859-018-2317-9.

3.

RNApdbee 2.0: multifunctional tool for RNA structure annotation.

Zok T, Antczak M, Zurkowski M, Popenda M, Blazewicz J, Adamiak RW, Szachniuk M.

Nucleic Acids Res. 2018 Jul 2;46(W1):W30-W35. doi: 10.1093/nar/gky314.

4.

New algorithms to represent complex pseudoknotted RNA structures in dot-bracket notation.

Antczak M, Popenda M, Zok T, Zurkowski M, Adamiak RW, Szachniuk M.

Bioinformatics. 2018 Apr 15;34(8):1304-1312. doi: 10.1093/bioinformatics/btx783.

5.

Application of Negative Curvature Hollow-Core Fiber in an Optical Fiber Sensor Setup for Multiphoton Spectroscopy.

Popenda MA, Stawska HI, Mazur LM, Jakubowski K, Kosolapov A, Kolyadin A, Bereś-Pawlik E.

Sensors (Basel). 2017 Oct 6;17(10). pii: E2278. doi: 10.3390/s17102278.

6.

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.

7.

New functionality of RNAComposer: an application to shape the axis of miR160 precursor structure.

Antczak M, Popenda M, Zok T, Sarzynska J, Ratajczak T, Tomczyk K, Adamiak RW, Szachniuk M.

Acta Biochim Pol. 2016;63(4):737-744. doi: 10.18388/abp.2016_1329. Epub 2016 Oct 14.

8.

New in silico approach to assessing RNA secondary structures with non-canonical base pairs.

Rybarczyk A, Szostak N, Antczak M, Zok T, Popenda M, Adamiak R, Blazewicz J, Szachniuk M.

BMC Bioinformatics. 2015 Sep 2;16:276. doi: 10.1186/s12859-015-0718-6.

9.

RNAssess--a web server for quality assessment of RNA 3D structures.

Lukasiak P, Antczak M, Ratajczak T, Szachniuk M, Popenda M, Adamiak RW, Blazewicz J.

Nucleic Acids Res. 2015 Jul 1;43(W1):W502-6. doi: 10.1093/nar/gkv557. Epub 2015 Jun 11.

10.

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.

11.

Automated 3D RNA structure prediction using the RNAComposer method for riboswitches.

Purzycka KJ, Popenda M, Szachniuk M, Antczak M, Lukasiak P, Blazewicz J, Adamiak RW.

Methods Enzymol. 2015;553:3-34. doi: 10.1016/bs.mie.2014.10.050. Epub 2015 Feb 4.

PMID:
25726459
12.

RNApdbee--a webserver to derive secondary structures from pdb files of knotted and unknotted RNAs.

Antczak M, Zok T, Popenda M, Lukasiak P, Adamiak RW, Blazewicz J, Szachniuk M.

Nucleic Acids Res. 2014 Jul;42(Web Server issue):W368-72. doi: 10.1093/nar/gku330. Epub 2014 Apr 25.

13.

Spiegelzymes® mirror-image hammerhead ribozymes and mirror-image DNAzymes, an alternative to siRNAs and microRNAs to cleave mRNAs in vivo?

Wyszko E, Mueller F, Gabryelska M, Bondzio A, Popenda M, Barciszewski J, Erdmann VA.

PLoS One. 2014 Jan 29;9(1):e86673. doi: 10.1371/journal.pone.0086673. eCollection 2014. Erratum in: PLoS One. 2014;9(3):e93798.

14.

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.

Nucleic Acids Res. 2013 Jul;41(12):5978-90. doi: 10.1093/nar/gkt318. Epub 2013 Apr 25.

15.

Prediction of hammerhead ribozyme intracellular activity with the catalytic core fingerprint.

Gabryelska MM, Wyszko E, Szymański M, Popenda M, Barciszewski J.

Biochem J. 2013 May 1;451(3):439-51. doi: 10.1042/BJ20121761.

PMID:
23418809
16.

2-Methylwyosine, a nucleoside with restricted anti conformation in the east region enforced by nucleobase moiety modification: synthesis and conformational analysis by NMR and molecular dynamics.

Baranowski D, Golankiewicz B, Folkman W, Popenda M.

Nucleosides Nucleotides Nucleic Acids. 2012;31(10):707-19. doi: 10.1080/15257770.2012.724133.

PMID:
23067123
17.

Automated 3D structure composition for large RNAs.

Popenda M, Szachniuk M, Antczak M, Purzycka KJ, Lukasiak P, Bartol N, Blazewicz J, Adamiak RW.

Nucleic Acids Res. 2012 Aug;40(14):e112. doi: 10.1093/nar/gks339. Epub 2012 Apr 26.

18.

RNA FRABASE 2.0: an advanced web-accessible database with the capacity to search the three-dimensional fragments within RNA structures.

Popenda M, Szachniuk M, Blazewicz M, Wasik S, Burke EK, Blazewicz J, Adamiak RW.

BMC Bioinformatics. 2010 May 6;11:231. doi: 10.1186/1471-2105-11-231.

19.

RNA FRABASE version 1.0: an engine with a database to search for the three-dimensional fragments within RNA structures.

Popenda M, Blazewicz M, Szachniuk M, Adamiak RW.

Nucleic Acids Res. 2008 Jan;36(Database issue):D386-91. Epub 2007 Oct 5.

20.

High-throughput method for the prediction of low-resolution, three-dimensional RNA structures.

Popenda M, Bielecki L, Adamiak RW.

Nucleic Acids Symp Ser (Oxf). 2006;(50):67-8.

PMID:
17150820
21.

High salt solution structure of a left-handed RNA double helix.

Popenda M, Milecki J, Adamiak RW.

Nucleic Acids Res. 2004 Aug 3;32(13):4044-54. Print 2004.

22.

An algorithm for an automatic NOE pathways analysis of 2D NMR spectra of RNA duplexes.

Adamiak RW, Blazewicz J, Formanowicz P, Gdaniec Z, Kasprzak M, Popenda M, Szachniuk M.

J Comput Biol. 2004;11(1):163-79.

PMID:
15072694
23.

An efficient route to novel 4,5-di- and 2,4,5-tri substituted imidazoles from imidazo[1,5-a]-1,3,5-triazine (5,8-diaza-7,9-dideazapurine) derivatives.

Golankiewicz B, Januszczyk P, Zeidler J, Popenda M.

Nucleosides Nucleotides Nucleic Acids. 2004;23(1-2):127-36.

PMID:
15043141
24.
25.

Acid promoted transformations of fluorescent luminarosine and its 2'-modified analogues.

Burdzy A, Skalski B, Paszyc S, Popenda M, Adamiak RW.

Acta Biochim Pol. 1998;45(4):941-8.

26.

Crystal structure of 2'-O-Me(CGCGCG)2, an RNA duplex at 1.30 A resolution. Hydration pattern of 2'-O-methylated RNA.

Adamiak DA, Milecki J, Popenda M, Adamiak RW, Dauter Z, Rypniewski WR.

Nucleic Acids Res. 1997 Nov 15;25(22):4599-607.

27.
28.

Z-RNA. The synthesis of 2'-O-[13C]methyl- and 5-methyl-analogs of ribo-CGCGCG.

Biała E, Milecki J, Kowalewski A, Popenda M, Antkowiak WZ, Adamiak RW.

Acta Biochim Pol. 1993;40(4):521-30.

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