Perahia D - Search Results

1

Consensus modes, a robust description of protein collective motions from multiple-minima normal mode analysis--application to the HIV-1 protease.

Batista PR, Robert CH, Maréchal JD, Hamida-Rebaï MB, Pascutti PG, Bisch PM, Perahia D. Batista PR, et al. Among authors: perahia d. Phys Chem Chem Phys. 2010 Mar 28;12(12):2850-9. doi: 10.1039/b919148h. Epub 2010 Feb 1. Phys Chem Chem Phys. 2010. PMID: 20449375

2

Exploring free energy landscapes of large conformational changes: molecular dynamics with excited normal modes.

Costa MG, Batista PR, Bisch PM, Perahia D. Costa MG, et al. Among authors: perahia d. J Chem Theory Comput. 2015 Jun 9;11(6):2755-67. doi: 10.1021/acs.jctc.5b00003. J Chem Theory Comput. 2015. PMID: 26575568

3

Free Energy Profiles along Consensus Normal Modes Provide Insight into HIV-1 Protease Flap Opening.

Batista PR, Pandey G, Pascutti PG, Bisch PM, Perahia D, Robert CH. Batista PR, et al. Among authors: perahia d. J Chem Theory Comput. 2011 Aug 9;7(8):2348-52. doi: 10.1021/ct200237u. Epub 2011 Jul 7. J Chem Theory Comput. 2011. PMID: 26606609

4

Conformational Equilibrium of CDK/Cyclin Complexes by Molecular Dynamics with Excited Normal Modes.

Floquet N, Costa MG, Batista PR, Renault P, Bisch PM, Raussin F, Martinez J, Morris MC, Perahia D. Floquet N, et al. Among authors: perahia d. Biophys J. 2015 Sep 15;109(6):1179-89. doi: 10.1016/j.bpj.2015.07.003. Epub 2015 Aug 6. Biophys J. 2015. PMID: 26255588 Free PMC article.

5

Normal mode analysis as a prerequisite for drug design: application to matrix metalloproteinases inhibitors.

Floquet N, Marechal JD, Badet-Denisot MA, Robert CH, Dauchez M, Perahia D. Floquet N, et al. Among authors: perahia d. FEBS Lett. 2006 Oct 2;580(22):5130-6. doi: 10.1016/j.febslet.2006.08.037. Epub 2006 Sep 1. FEBS Lett. 2006. PMID: 16962102 Free article.

6

Use of normal modes for structural modeling of proteins: the case study of rat heme oxygenase 1.

Maréchal JD, Perahia D. Maréchal JD, et al. Among authors: perahia d. Eur Biophys J. 2008 Sep;37(7):1157-65. doi: 10.1007/s00249-008-0279-y. Epub 2008 Feb 20. Eur Biophys J. 2008. PMID: 18286277

7

Editorial: Integrative Structural Biology of Proteins and Macromolecular Assemblies: Bridging Experiments and Simulations.

Batista PR, Oliveira Neto M, Perahia D. Batista PR, et al. Among authors: perahia d. Front Mol Biosci. 2022 Jun 27;9:947582. doi: 10.3389/fmolb.2022.947582. eCollection 2022. Front Mol Biosci. 2022. PMID: 35832739 Free PMC article. No abstract available.

8

Concerted conformational dynamics and water movements in the ghrelin G protein-coupled receptor.

Louet M, Casiraghi M, Damian M, Costa MG, Renault P, Gomes AA, Batista PR, M'Kadmi C, Mary S, Cantel S, Denoyelle S, Ben Haj Salah K, Perahia D, Bisch PM, Fehrentz JA, Catoire LJ, Floquet N, Banères JL. Louet M, et al. Among authors: perahia d. Elife. 2021 Sep 3;10:e63201. doi: 10.7554/eLife.63201. Elife. 2021. PMID: 34477105 Free PMC article.

9

Internal cavities and ligand passageways in human hemoglobin characterized by molecular dynamics simulations.

Mouawad L, Maréchal JD, Perahia D. Mouawad L, et al. Among authors: perahia d. Biochim Biophys Acta. 2005 Aug 5;1724(3):385-93. doi: 10.1016/j.bbagen.2005.05.014. Biochim Biophys Acta. 2005. PMID: 15963643

10

A DFT study on the relative affinity for oxygen of the alpha and beta subunits of hemoglobin.

Maréchal JD, Maseras F, Lledós A, Mouawad L, Perahia D. Maréchal JD, et al. Among authors: perahia d. J Comput Chem. 2006 Sep;27(12):1446-53. doi: 10.1002/jcc.20427. J Comput Chem. 2006. PMID: 16807972

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