Perahia D - Search Results

1

Multimolecular complexes of the phosphodiester anion with Zn(II) or Mg(II) and water molecules-Preliminary validations of a polarizable potential by ab initio quantum chemistry.

Gresh N, Perahia D. Gresh N, et al. Among authors: perahia d. J Comput Chem. 2021 Jul 30;42(20):1430-1446. doi: 10.1002/jcc.26555. Epub 2021 Jun 8. J Comput Chem. 2021. PMID: 34101861

2

Polarizable molecular mechanics studies of Cu(I)/Zn(II) superoxide dismutase: bimetallic binding site and structured waters.

Gresh N, El Hage K, Perahia D, Piquemal JP, Berthomieu C, Berthomieu D. Gresh N, et al. Among authors: perahia d. J Comput Chem. 2014 Nov 5;35(29):2096-106. doi: 10.1002/jcc.23724. Epub 2014 Sep 11. J Comput Chem. 2014. PMID: 25212748

3

Complexes of a Zn-metalloenzyme binding site with hydroxamate-containing ligands. A case for detailed benchmarkings of polarizable molecular mechanics/dynamics potentials when the experimental binding structure is unknown.

Gresh N, Perahia D, de Courcy B, Foret J, Roux C, El-Khoury L, Piquemal JP, Salmon L. Gresh N, et al. Among authors: perahia d. J Comput Chem. 2016 Dec 15;37(32):2770-2782. doi: 10.1002/jcc.24503. Epub 2016 Oct 4. J Comput Chem. 2016. PMID: 27699809

4

A New Strategy for Atomic Flexible Fitting in Cryo-EM Maps by Molecular Dynamics with Excited Normal Modes (MDeNM-EMfit).

Costa MGS, Fagnen C, Vénien-Bryan C, Perahia D. Costa MGS, et al. Among authors: perahia d. J Chem Inf Model. 2020 May 26;60(5):2419-2423. doi: 10.1021/acs.jcim.9b01148. Epub 2020 Jan 28. J Chem Inf Model. 2020. PMID: 31944765

5

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

6

ABCG2/BCRP transport mechanism revealed through kinetically excited targeted molecular dynamics simulations.

Dudas B, Decleves X, Cisternino S, Perahia D, Miteva MA. Dudas B, et al. Among authors: perahia d. Comput Struct Biotechnol J. 2022 Jul 29;20:4195-4205. doi: 10.1016/j.csbj.2022.07.035. eCollection 2022. Comput Struct Biotechnol J. 2022. PMID: 36016719 Free PMC article.

7

Insights into the substrate binding mechanism of SULT1A1 through molecular dynamics with excited normal modes simulations.

Dudas B, Toth D, Perahia D, Nicot AB, Balog E, Miteva MA. Dudas B, et al. Among authors: perahia d. Sci Rep. 2021 Jun 23;11(1):13129. doi: 10.1038/s41598-021-92480-w. Sci Rep. 2021. PMID: 34162941 Free PMC article.

8

Cryo-electron microscopy unveils unique structural features of the human Kir2.1 channel.

Fernandes CAH, Zuniga D, Fagnen C, Kugler V, Scala R, Péhau-Arnaudet G, Wagner R, Perahia D, Bendahhou S, Vénien-Bryan C. Fernandes CAH, et al. Among authors: perahia d. Sci Adv. 2022 Sep 23;8(38):eabq8489. doi: 10.1126/sciadv.abq8489. Epub 2022 Sep 23. Sci Adv. 2022. PMID: 36149965 Free PMC article.

9

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

10

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.

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