Lavery R - Search Results

1

A free energy pathway for the interaction of the SRY protein with its binding site on DNA from atomistic simulations.

Bouvier B, Lavery R. Bouvier B, et al. Among authors: lavery r. J Am Chem Soc. 2009 Jul 29;131(29):9864-5. doi: 10.1021/ja901761a. J Am Chem Soc. 2009. PMID: 19580270

2

Protein-DNA binding specificity: a grid-enabled computational approach applied to single and multiple protein assemblies.

Zakrzewska K, Bouvier B, Michon A, Blanchet C, Lavery R. Zakrzewska K, et al. Among authors: lavery r. Phys Chem Chem Phys. 2009 Dec 7;11(45):10712-21. doi: 10.1039/b910888m. Epub 2009 Oct 7. Phys Chem Chem Phys. 2009. PMID: 20145815

3

Multistep drug intercalation: molecular dynamics and free energy studies of the binding of daunomycin to DNA.

Wilhelm M, Mukherjee A, Bouvier B, Zakrzewska K, Hynes JT, Lavery R. Wilhelm M, et al. Among authors: lavery r. J Am Chem Soc. 2012 May 23;134(20):8588-96. doi: 10.1021/ja301649k. Epub 2012 May 11. J Am Chem Soc. 2012. PMID: 22548344

4

Protein-DNA recognition triggered by a DNA conformational switch.

Bouvier B, Zakrzewska K, Lavery R. Bouvier B, et al. Among authors: lavery r. Angew Chem Int Ed Engl. 2011 Jul 11;50(29):6516-8. doi: 10.1002/anie.201101417. Epub 2011 May 30. Angew Chem Int Ed Engl. 2011. PMID: 21626631 No abstract available.

5

Base flipping in DNA: pathways and energetics studied with molecular dynamic simulations.

Várnai P, Lavery R. Várnai P, et al. Among authors: lavery r. J Am Chem Soc. 2002 Jun 26;124(25):7272-3. doi: 10.1021/ja025980x. J Am Chem Soc. 2002. PMID: 12071727

6

Nucleic acid base pair dynamics: the impact of sequence and structure using free-energy calculations.

Giudice E, Lavery R. Giudice E, et al. Among authors: lavery r. J Am Chem Soc. 2003 Apr 30;125(17):4998-9. doi: 10.1021/ja034095r. J Am Chem Soc. 2003. PMID: 12708848

7

On the molecular mechanism of drug intercalation into DNA: a simulation study of the intercalation pathway, free energy, and DNA structural changes.

Mukherjee A, Lavery R, Bagchi B, Hynes JT. Mukherjee A, et al. Among authors: lavery r. J Am Chem Soc. 2008 Jul 30;130(30):9747-55. doi: 10.1021/ja8001666. Epub 2008 Jul 9. J Am Chem Soc. 2008. PMID: 18611009

8

Dynamics and recognition within a protein-DNA complex: a molecular dynamics study of the SKN-1/DNA interaction.

Etheve L, Martin J, Lavery R. Etheve L, et al. Among authors: lavery r. Nucleic Acids Res. 2016 Feb 18;44(3):1440-8. doi: 10.1093/nar/gkv1511. Epub 2015 Dec 31. Nucleic Acids Res. 2016. PMID: 26721385 Free PMC article.

9

Decomposing protein-DNA binding and recognition using simplified protein models.

Etheve L, Martin J, Lavery R. Etheve L, et al. Among authors: lavery r. Nucleic Acids Res. 2017 Sep 29;45(17):10270-10283. doi: 10.1093/nar/gkx627. Nucleic Acids Res. 2017. PMID: 28973439 Free PMC article.

10

Recognizing DNA.

Lavery R. Lavery R. Q Rev Biophys. 2005 Nov;38(4):339-44. doi: 10.1017/S0033583505004105. Epub 2006 Mar 6. Q Rev Biophys. 2005. PMID: 16515738

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