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Items: 1 to 20 of 52

1.

Scanning of 16S Ribosomal RNA for Peptide Nucleic Acid Targets.

Górska A, Markowska-Zagrajek A, Równicki M, Trylska J.

J Phys Chem B. 2016 May 4. [Epub ahead of print]

PMID:
27105576
2.

Conformational space of clindamycin studied by ab initio and full-atom molecular dynamics.

Kulczycka-Mierzejewska K, Trylska J, Sadlej J.

J Mol Model. 2016 Jan;22(1):20. doi: 10.1007/s00894-015-2881-0. Epub 2016 Jan 5.

PMID:
26733483
3.

Vitamin B12 Suitably Tailored for Disulfide-Based Conjugation.

Wierzba A, Wojciechowska M, Trylska J, Gryko D.

Bioconjug Chem. 2016 Jan 20;27(1):189-97. doi: 10.1021/acs.bioconjchem.5b00599. Epub 2016 Jan 4.

PMID:
26693734
4.

Kinetics of trypsin-catalyzed hydrolysis determined by isothermal titration calorimetry.

Maximova K, Trylska J.

Anal Biochem. 2015 Oct 1;486:24-34. doi: 10.1016/j.ab.2015.06.027. Epub 2015 Jun 25.

PMID:
26119333
5.

MINT: software to identify motifs and short-range interactions in trajectories of nucleic acids.

Górska A, Jasiński M, Trylska J.

Nucleic Acids Res. 2015 Sep 30;43(17):e114. doi: 10.1093/nar/gkv559. Epub 2015 May 29.

6.

RedMDStream: Parameterization and Simulation Toolbox for Coarse-Grained Molecular Dynamics Models.

Leonarski F, Trylska J.

Biophys J. 2015 Apr 21;108(8):1843-7. doi: 10.1016/j.bpj.2015.03.023.

7.

Conformational dynamics of bacterial and human cytoplasmic models of the ribosomal A-site.

Panecka J, Šponer J, Trylska J.

Biochimie. 2015 May;112:96-110. doi: 10.1016/j.biochi.2015.02.021. Epub 2015 Mar 3.

PMID:
25748164
8.

Electrostatic interactions in aminoglycoside-RNA complexes.

Kulik M, Goral AM, Jasiński M, Dominiak PM, Trylska J.

Biophys J. 2015 Feb 3;108(3):655-65. doi: 10.1016/j.bpj.2014.12.020.

9.

Interplay of the bacterial ribosomal A-site, S12 protein mutations and paromomycin binding: a molecular dynamics study.

Panecka J, Mura C, Trylska J.

PLoS One. 2014 Nov 7;9(11):e111811. doi: 10.1371/journal.pone.0111811. eCollection 2014.

10.

Role of S-turn2 in the structure, dynamics, and function of mitochondrial ribosomal A-site. A bioinformatics and molecular dynamics simulation study.

Panecka J, Havrila M, Réblová K, Šponer J, Trylska J.

J Phys Chem B. 2014 Jun 19;118(24):6687-701. doi: 10.1021/jp5030685. Epub 2014 Jun 6.

PMID:
24845793
11.

Interactions of amikacin with the RNA model of the ribosomal A-site: computational, spectroscopic and calorimetric studies.

Dudek M, Romanowska J, Wituła T, Trylska J.

Biochimie. 2014 Jul;102:188-202. doi: 10.1016/j.biochi.2014.03.009. Epub 2014 Apr 24.

PMID:
24769038
12.

Evolutionary Algorithm in the Optimization of a Coarse-Grained Force Field.

Leonarski F, Trovato F, Tozzini V, Leś A, Trylska J.

J Chem Theory Comput. 2013 Nov 12;9(11):4874-89. doi: 10.1021/ct4005036. Epub 2013 Oct 21.

PMID:
26583407
13.

Using sequence-specific oligonucleotides to inhibit bacterial rRNA.

Trylska J, Thoduka SG, Dąbrowska Z.

ACS Chem Biol. 2013;8(6):1101-9. doi: 10.1021/cb400163t. Epub 2013 May 10. Review.

PMID:
23631412
14.

Comparing aminoglycoside binding sites in bacterial ribosomal RNA and aminoglycoside modifying enzymes.

Romanowska J, Reuter N, Trylska J.

Proteins. 2013 Jan;81(1):63-80. doi: 10.1002/prot.24163. Epub 2012 Sep 26.

PMID:
22907688
15.

Determining Geometrically Stable Domains in Molecular Conformation Sets.

Romanowska J, Nowiński KS, Trylska J.

J Chem Theory Comput. 2012 Aug 14;8(8):2588-99. doi: 10.1021/ct300206j. Epub 2012 Aug 2.

PMID:
26592104
16.

Contributions of far-field hydrodynamic interactions to the kinetics of electrostatically driven molecular association.

Długosz M, Antosiewicz JM, Zieliński P, Trylska J.

J Phys Chem B. 2012 May 10;116(18):5437-47. doi: 10.1021/jp301265y. Epub 2012 Apr 26.

PMID:
22512305
17.

Unwrapping of nucleosomal DNA ends: a multiscale molecular dynamics study.

Voltz K, Trylska J, Calimet N, Smith JC, Langowski J.

Biophys J. 2012 Feb 22;102(4):849-58. doi: 10.1016/j.bpj.2011.11.4028. Epub 2012 Feb 21.

18.

Quantum mechanical studies of lincosamides.

Kulczycka-Mierzejewska K, Trylska J, Sadlej J.

J Mol Model. 2012 Jun;18(6):2727-40. doi: 10.1007/s00894-011-1272-4. Epub 2011 Nov 25.

19.

Secondary structures of native and pathogenic huntingtin N-terminal fragments.

Długosz M, Trylska J.

J Phys Chem B. 2011 Oct 13;115(40):11597-608. doi: 10.1021/jp206373g. Epub 2011 Sep 21.

PMID:
21910495
20.

Understanding the origins of bacterial resistance to aminoglycosides through molecular dynamics mutational study of the ribosomal A-site.

Romanowska J, McCammon JA, Trylska J.

PLoS Comput Biol. 2011 Jul;7(7):e1002099. doi: 10.1371/journal.pcbi.1002099. Epub 2011 Jul 21.

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