David Perahia
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Explore the profile of David Perahia including associated specialties, affiliations and a list of published articles.
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68
Citations
622
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Recent Articles
1.
S Gomes A, Costa M, Louet M, Floquet N, Bisch P, Perahia D
J Chem Theory Comput
. 2024 Dec;
20(24):10770-10786.
PMID: 39663763
Proteins are dynamic entities that adopt diverse conformations, which play a pivotal role in their function. Understanding these conformations is essential, and protein collective motions, particularly those captured by normal...
2.
Dahmani Z, Scott A, Venien-Bryan C, Perahia D, Costa M
J Chem Inf Model
. 2024 Jun;
64(13):5151-5160.
PMID: 38907694
Molecular Dynamics Flexible Fitting (MDFF) is a widely used tool to refine high-resolution structures into cryo-EM density maps. Despite many successful applications, MDFF is still limited by its high computational...
3.
Czigleczki J, de Resende Lara P, Dudas B, Jang H, Perahia D, Nussinov R, et al.
Front Mol Biosci
. 2023 Feb;
10:1111574.
PMID: 36726377
The small GTPase Ran is the main regulator of the nucleo-cytoplasmic import and export through the nuclear pore complex. It functions as a molecular switch cycling between the GDP-bound inactive...
4.
Costa M, Batista P, Gomes A, Bastos L, Louet M, Floquet N, et al.
J Chem Theory Comput
. 2023 Jan;
PMID: 36622950
Molecular dynamics with excited normal modes (MDeNM) is an enhanced sampling method for exploring conformational changes in proteins with minimal biases. The excitation corresponds to injecting kinetic energy along normal...
5.
Dudas B, Bagdad Y, Picard M, Perahia D, Miteva M
iScience
. 2022 Oct;
25(11):105290.
PMID: 36304105
UDP-glucuronosyltransferases (UGTs) are responsible for 35% of the phase II drug metabolism. In this study, we focused on UGT1A1, which is a key UGT isoform. Strong inhibition of UGT1A1 may...
6.
Fernandes C, Zuniga D, Fagnen C, Kugler V, Scala R, Pehau-Arnaudet G, et al.
Sci Adv
. 2022 Sep;
8(38):eabq8489.
PMID: 36149965
We present the first structure of the human Kir2.1 channel containing both transmembrane domain (TMD) and cytoplasmic domain (CTD). Kir2.1 channels are strongly inward-rectifying potassium channels that play a key...
7.
Batista P, Oliveira Neto M, Perahia D
Front Mol Biosci
. 2022 Jul;
9:947582.
PMID: 35832739
No abstract available.
8.
Kaynak B, Krieger J, Dudas B, Dahmani Z, Costa M, Balog E, et al.
Front Mol Biosci
. 2022 Feb;
9:832847.
PMID: 35187088
Recent years have seen several hybrid simulation methods for exploring the conformational space of proteins and their complexes or assemblies. These methods often combine fast analytical approaches with computationally expensive...
9.
Fagnen C, Bannwarth L, Oubella I, Zuniga D, Haouz A, Forest E, et al.
Int J Mol Sci
. 2022 Jan;
23(1).
PMID: 35008764
ATP-sensitive potassium (K-ATP) channels are ubiquitously expressed on the plasma membrane of cells in several organs, including the heart, pancreas, and brain, and they govern a wide range of physiological...
10.
Louet M, Casiraghi M, Damian M, Costa M, Renault P, Gomes A, et al.
Elife
. 2021 Sep;
10.
PMID: 34477105
There is increasing support for water molecules playing a role in signal propagation through G protein-coupled receptors (GPCRs). However, exploration of the hydration features of GPCRs is still in its...