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Results: 1 to 20 of 45

1.

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.

PMID:
25902423
2.

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
3.

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.

PMID:
25650932
4.

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.

5.

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
6.

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
7.

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
8.

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
9.

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
10.

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.

11.

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.

12.

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
13.

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.

14.

Brownian dynamics simulations on CPU and GPU with BD_BOX.

Długosz M, Zieliński P, Trylska J.

J Comput Chem. 2011 Sep;32(12):2734-44. doi: 10.1002/jcc.21847. Epub 2011 Jun 2.

PMID:
21638295
15.

Diffusion in crowded biological environments: applications of Brownian dynamics.

Długosz M, Trylska J.

BMC Biophys. 2011 Mar 2;4:3. doi: 10.1186/2046-1682-4-3.

16.

Brownian dynamics study of the association between the 70S ribosome and elongation factor G.

Długosz M, Huber GA, McCammon JA, Trylska J.

Biopolymers. 2011 Sep;95(9):616-27. doi: 10.1002/bip.21619. Epub 2011 Mar 10.

17.

Coarse-grained models to study dynamics of nanoscale biomolecules and their applications to the ribosome.

Trylska J.

J Phys Condens Matter. 2010 Nov 17;22(45):453101. doi: 10.1088/0953-8984/22/45/453101. Epub 2010 Oct 28. Review.

PMID:
21339588
18.

Molecular dynamics of potential rRNA binders: single-stranded nucleic acids and some analogues.

Panecka J, Mura C, Trylska J.

J Phys Chem B. 2011 Jan 27;115(3):532-46. doi: 10.1021/jp106404u. Epub 2010 Dec 30.

PMID:
21192664
19.

Molecular dynamics of ribosomal elongation factors G and Tu.

Kulczycka K, Długosz M, Trylska J.

Eur Biophys J. 2011 Mar;40(3):289-303. doi: 10.1007/s00249-010-0647-2. Epub 2010 Dec 9.

20.

Simulating activity of the bacterial ribosome.

Trylska J.

Q Rev Biophys. 2009 Nov;42(4):301-16. doi: 10.1017/S0033583510000028. Review.

PMID:
20450532
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