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Results: 16

1.

Mapping the spatial neighborhood of the regulatory 6S RNA bound to Escherichia coli RNA polymerase holoenzyme.

Steuten B, Setny P, Zacharias M, Wagner R.

J Mol Biol. 2013 Oct 9;425(19):3649-61. doi: 10.1016/j.jmb.2013.07.008. Epub 2013 Jul 15.

PMID:
23867276
[PubMed - indexed for MEDLINE]
2.

Solvent fluctuations in hydrophobic cavity-ligand binding kinetics.

Setny P, Baron R, Michael Kekenes-Huskey P, McCammon JA, Dzubiella J.

Proc Natl Acad Sci U S A. 2013 Jan 22;110(4):1197-202. doi: 10.1073/pnas.1221231110. Epub 2013 Jan 7.

PMID:
23297241
[PubMed - indexed for MEDLINE]
Free PMC Article
3.

Water structure, dynamics, and spectral signatures: changes upon model cavity-ligand recognition.

Baron R, Setny P, Paesani F.

J Phys Chem B. 2012 Nov 26;116(46):13774-80. doi: 10.1021/jp309373q. Epub 2012 Nov 7.

PMID:
23102165
[PubMed - indexed for MEDLINE]
4.

Protein-DNA docking with a coarse-grained force field.

Setny P, Bahadur RP, Zacharias M.

BMC Bioinformatics. 2012 Sep 11;13:228. doi: 10.1186/1471-2105-13-228.

PMID:
22966980
[PubMed - indexed for MEDLINE]
Free PMC Article
5.

A coarse-grained force field for Protein-RNA docking.

Setny P, Zacharias M.

Nucleic Acids Res. 2011 Nov;39(21):9118-29. doi: 10.1093/nar/gkr636. Epub 2011 Aug 16.

PMID:
21846771
[PubMed - indexed for MEDLINE]
Free PMC Article
6.

How Can Hydrophobic Association Be Enthalpy Driven?

Setny P, Baron R, McCammon JA.

J Chem Theory Comput. 2010 Sep 14;6(9):2866-2871. Epub 2010 Aug 24.

PMID:
20844599
[PubMed]
Free PMC Article
7.

Water in cavity-ligand recognition.

Baron R, Setny P, McCammon JA.

J Am Chem Soc. 2010 Sep 1;132(34):12091-7. doi: 10.1021/ja1050082.

PMID:
20695475
[PubMed - indexed for MEDLINE]
Free PMC Article
8.

Hydration in discrete water. A mean field, cellular automata based approach to calculating hydration free energies.

Setny P, Zacharias M.

J Phys Chem B. 2010 Jul 8;114(26):8667-75. doi: 10.1021/jp102462s.

PMID:
20552986
[PubMed - indexed for MEDLINE]
9.

Dewetting-controlled binding of ligands to hydrophobic pockets.

Setny P, Wang Z, Cheng LT, Li B, McCammon JA, Dzubiella J.

Phys Rev Lett. 2009 Oct 30;103(18):187801. Epub 2009 Oct 30.

PMID:
19905832
[PubMed - indexed for MEDLINE]
Free PMC Article
10.

Interfaces and hydrophobic interactions in receptor-ligand systems: A level-set variational implicit solvent approach.

Cheng LT, Wang Z, Setny P, Dzubiella J, Li B, McCammon JA.

J Chem Phys. 2009 Oct 14;131(14):144102. doi: 10.1063/1.3242274.

PMID:
19831428
[PubMed - indexed for MEDLINE]
Free PMC Article
11.

Search for novel aminoglycosides by combining fragment-based virtual screening and 3D-QSAR scoring.

Setny P, Trylska J.

J Chem Inf Model. 2009 Feb;49(2):390-400.

PMID:
19434840
[PubMed - indexed for MEDLINE]
Free PMC Article
12.

Molecular dynamics study of the ribosomal A-site.

Romanowska J, Setny P, Trylska J.

J Phys Chem B. 2008 Nov 27;112(47):15227-43. doi: 10.1021/jp806814s.

PMID:
18973356
[PubMed - indexed for MEDLINE]
Free PMC Article
13.

Hydrophobic interactions between methane and a nanoscopic pocket: three dimensional distribution of potential of mean force revealed by computer simulations.

Setny P.

J Chem Phys. 2008 Mar 28;128(12):125105. doi: 10.1063/1.2839885.

PMID:
18376980
[PubMed - indexed for MEDLINE]
14.
15.

Water properties inside nanoscopic hydrophobic pocket studied by computer simulations.

Setny P, Geller M.

J Chem Phys. 2006 Oct 14;125(14):144717.

PMID:
17042641
[PubMed - indexed for MEDLINE]
16.

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