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Publications du groupe de David Perahia


Eric Allison Philot, David da Mata Lopes, Aryane Tofanello de Souza, Antônio Sérgio Kimus Braz, Iseli Lourenço Nantes, Tiago Rodrigues, David Perahia, Maria A Miteva, Luis Paulo Barbour Scot. Binding of phenothiazines into allosteric hydrophobic pocket of human thioredoxin 1. European Biophysics Journal 45, 279-286, 2016.

Nohad Gresh, David Perahia, Benoit de Courcy, Johanna Foret, Céline Roux, Lea ElKhoury, JeanPhilip Piquemal, Laurent Salmon. Complexes of a Znmetalloenzyme binding site with hydroxamatecontaining ligands. A case for detailed benchmarkings of polarizable molecular mechanics/dynamics potentials when the experimental binding structure is unknown. Journal of computational chemistry 37, 2770-2782, 2016.


Gautier Moroy, Olivier Sperandio, Shakti Rielland, Saurabh Khemka, Karen Druart, Divij Goyal, David Perahia, Maria A Miteva. Sampling of conformational ensemble for virtual screening using molecular dynamics simulations and normal mode analysis. Future medicinal chemistry 7, 2317-2331, 2015

P Renault, D Perahia, PM Bisch. Allosteric modulation of the major cathepsin L of Trypanosoma brucei by molecular simulation. EUROPEAN BIOPHYSICS JOURNAL WITH BIOPHYSICS LETTERS 44, S172-S172, 2015

Riley Blake T., Broendum Sebastian S., Reboul Cyril F., Cowieson Nathan P., Costa Mauricio G. S., Kass Itamar, Jackson Colin, Perahia David, Buckle Ashley M., Mcgowan Sheena. Dynamic Motion and Communication in the Streptococcal C1 Phage Lysin, PlyC. PLOS ONE DOI:10.1371/journal.pone. 0140219 October 15, 2015 [PDF]

Nicolas Floquet, Mauricio G S Costa, Paulo R Batista, Pedro Renault, Paulo M Bisch,  Florent Raussin, Jean Martinez, May C Morris, David Perahia. Conformational Equilibrium of CDK/Cyclin Complexes by Molecular Dynamics with Excited Normal Modes. Biophysical Journal 08/2015; 109(3). DOI:10.1016/j.bpj.2015.07.003 · (IF = 3.97)

Valderes De Conto, Antônio S.K. Braz, David Perahia, Luis P.B. Scott. Recovery of the wild type atomic flexibility in the HIV-1 protease double mutants. Journal of molecular graphics & modelling 04/2015; 59. DOI:10.1016/j.jmgm.2015.04.006 · (IF = 2.02)

Mauricio Garcia de Souza Costa, Paulo Ricardo Batista, Paulo Mascarello Bisch, David Perahia. Exploring Free Energy Landscapes of Large Conformational Changes: Molecular Dynamics with Excited Normal Modes. Journal of Chemical Theory and Computation 04/2015; 11(6). DOI:10.1021/acs.jctc.5b00003 · (IF = 5.31)

Marjorie Damian, Sophie Mary, Mathieu Maingot, Céline M'Kadmi, Didier Gagne, Jean-Philippe Leyris, Séverine Denoyelle, Gérald Gaibelet, Laurent Gavara, Mauricio Garcia de Souza Costa, David Perahia, Eric Trinquet, Bernard Mouillac, Ségolène Galandrin, Céline Galès, Jean-Alain Fehrentz, Nicolas Floquet, Jean Martinez, Jacky Marie, Jean-Louis Banères. Ghrelin receptor conformational dynamics regulate the transition from a preassembled to an active receptor:Gq complex. Proceedings of the National Academy of Sciences 01/2015; 112(5). DOI:10.1073/pnas.1414618112 · (IF = 9.81)

Nohad Gresh, Krystel El Hage, Elodie Goldwaser, Benoit de Courcy, Robin Chaudret, David Perahia, Christophe Narth, Louis Lagardere, Filippo Lipparini, Jean-Philip Piquemal. Addressing the issues of non-isotropy and non-additivity in the development of quantum chemistry-grounded polarizable molecular mechanics. Quantum Modeling of Complex Molecular Systems, Edited by J. L. Rivail, M. Ruiz-Lopez, X. Assfeld, 01/2015; Springer.

Elbahnsi A, Mauffret O, Perahia D, Hartmann B, Oguey C. 25 New insights on nucleic acids - protein interfaces revealed by VLDM, a geometrical approach. J Biomol Struct Dyn. 2015 May; 33 (sup1):14-15


Nohad Gresh, Krystel El Hage, David Perahia, Jean-Philip Piquemal, Catherine Berthomieu, Dorothée Berthomieu, Polarizable Molecular Mechanics Studies of Cu(I)/Zn(II) Superoxide Dismutase: Bimetallic Binding Site and Structured Waters. Journal of Computational Chemistry 11/2014; DOI:10.1002/jcc.23724 · (IF = 3.60)

Itamar Kass, David E. Hoke, Mauricio G. S. Costa, Cyril F. Reboul, Benjamin T. Porebski, Nathan P. Cowieson, Hervé Leh, Eugenia Pennacchietti, Julia McCoey, Oded Kleifeld, Carla Borri Voltattorni, David Langley, Brendan Roome, Ian R. Mackay, Daniel Christ, David Perahia, Malcolm Buckle, Alessandro Paiardini, Daniela De Biase, Ashley M. Buckle. Cofactor-dependent conformational heterogeneity of GAD65 and its role in autoimmunity and neurotransmitter homeostasis. Proceedings of the National Academy of Sciences 06/2014; 111(25). DOI:10.1073/pnas.1403182111 · (IF = 9.81)


Marta Menegazzi, Sofia Mariotto, Martina Dal Bosco, Elena Darra, Nadia Vaiana, Kazuo Shoji, Abdel-Azeim Safwat, Jean Didier Marechal, David Perahia, Hisanori Suzuki, Sergio Romeo. Direct interaction of natural and synthetic catechins with Signal Transducer Activator of Transcription-1 affects both its phosphorylation and activity. FEBS Journal. 11/2013; DOI:10.1111/febs.12618 (IF = 3.79)

Eric Quiniou, Paul Guichard, David Perahia, Sergio Marco, Liliane Mouawad. An Atomistic View of Microtubule Stabilization by GTP. Structure. 2013 May 7;21(5):833-43. (IF=6.35)

Louet M, Karakas E, Perret A, Perahia D, Martinez J, Floquet N. Conformational restriction of G-proteins Coupled Receptors (GPCRs) upon complexation to G-proteins: A putative activation mode of GPCRs? FEBS letters 07/2013; 587(16). DOI:10.1016/j.febslet.2013.06.052 · (IF=3.54)

Eric Allison Philot, David Perahia, Antônio Sérgio Kimus Braz, Mauricio Garcia de Souza Costa, Luis Paulo Barbour Scott. Binding sites and hydrophobic pockets in Human Thioredoxin 1 determined by normal mode analysis. Journal of Structural Biology 09/2013. (IF= 3.41).

Antônio S K Braz, Patrícia Tufanetto, David Perahia, Luis P B Scott. Relation between flexibility and positively selected HIV-1 protease mutants against inhibitors. Proteins. 07/2012; (IF=3.09)

Bosco K Ho, David Perahia, Ashley M Buckle. Hybrid approaches to molecular simulation. Current opinion in structural biology. 05/2012; 22(3):386-93. (IF=9.34)

Angélica Nakagawa Lima, Eric Allison Philot, David Perahia, Antonio Sérgio Kimus Braz, Luis P. B. Scott. GANM: A protein-ligand docking approach based on genetic algorithm and normal modes. Applied Mathematics and Computation. 01/2012; 219(2):511-520.

Balog, E., Perahia, D., Smith, J.C., and Merzel, F. (2011). Vibrational softening of a protein on ligand binding. J Phys Chem B 115, 6811-6817. (IF = 4.189).

Z. Palmai, D. Perahia, C. Lionne, J. Fidy, E. Balog and L. Chaloin. (2011) Ligand chirality effects on the catalytic efficiency of human 3-phosphoglycerate kinase: comparison between D- and L- nucleotides. Arch. Biochem. Biophys. In press (IF= 3.046)

Batista P. R., Pandey G., Pascutti P. G., Bisch P. M., Perahia D. and Robert C. H. (2011). Free Energy Profiles along Consensus Normal Modes Provide Insight into HIV-1 Protease Flap Opening. JCTC. in press (IF= 5.138)

M. Louet, D. Perahia, J. Martinez and N. Floquet (2011). A concerted mechanism for opening the GDP binding pocket and release of the nucleotide in hetero-trimeric G-proteins. J. Mol. Biol. In press. (IF = 3.871)

Batista, P. R., Robert, C. H., Marechal, J. D., Ben Hamida-Rebai, M., Pascutti, P. G., Bisch, P. M., & Perahia, D. (2010). Consensus modes, a robust description of protein collective motions from multiple-minima normal mode analysis-application to the HIV-1 protease. Physical Chemistry Chemical Physics 12, 2850-2859. (IF= 4.116).

Floquet, N., MiKadmi, C., Perahia, D., Gagne, D., Berge, G., Marie, J., Baneres, J. L., Galleyrand, J. C., Fehrentz, J. A., & Martinez, J. (2010). Activation of the Ghrelin Receptor is Described by a Privileged Collective Motion: A Model for Constitutive and Agonist-induced Activation of a Sub-class A G-Protein Coupled Receptor (GPCR). Journal of Molecular Biology 395, 769-784 (IF= 4.303)

Sperandio, O., Mouawad, L., Pinto, E., Villoutreix, B. O., Perahia, D., & Miteva, M. A. (2010). How to choose relevant multiple receptor conformations for virtual screening: a test case of Cdk2 and normal mode analysis. Eur. Biophys. J.39, 1365-1372.  (IF= 1.950)

Scarabelli, T.M.,  S. Mariotto, S. Abdel-Azeim, K. Shoji, E. Darra, A. Stephanou, Chen-Scarabelli, J.D. Marechal, R. Knight, A. Ciampa, L. Saravolatz, A.C. De Prati, Z. Yuan, E. Cavalieri, M. Menegazzi, D. Latchman, C. Pizza, D. Perahia, H. Suzuki. (2009). Targeting stat1 by myricetin and delphinidin provides efficient protection of the heart from ischemia/reperfusion-induced injury. Febs lett. 583, 531-541. (IF= 3.319).

Floquet, N., P. Durand, B. Maigret , B. Badet, M-A. Badet-Denisot, D. Perahia. (2009).Collective motions in Glucosamine-6-Phosphate Synthase: influence of ligand binding and their role in ammonia channelling and opening of the Fructose-6P binding site. J. Mol. Biol. 385 653-664  (IF= 4.303).

Palmai Z, L. Chaloin, C. Lionne, J. Fidy,  D. Perahia,  E. Balog. (2009). Substrate binding modifies the hinge bending characteristics of human 3-phosphoglycerate kinase: A molecular dynamics study. Proteins, 77319-329. (IF= 4.8)

Darra, E.,  S. Abdel-Azeim, A. Manara, K. Shoji, J-D. Marechal, S. Mariotto, E. Cavalieri, L. Perbellini, C. Pizza, D. Perahia, M. Crimi, H. Suzuki. (2008).Insight Into The Apoptosis-Inducing Action Of Bisabolol Towards Malignant Tumor Cells: Involvment Of Lipid Rafts And Bid. Arch. Biochem. Biophys 476, 113-123. (IF= 3.046).

Maréchal J.D., D. Perahia. (2008) Use of Normal Modes for structural modeling of proteins: the case study of rat heme oxygenase. Eur. J. Biophys. 371157-1165. (IF= 2.437).

Floquet N., S. Dedieu, L. Martiny, M. Dauchez, D. Perahia. (2008) Human thrombospondin's (TSP-1) C-terminal domain opens to interact with the CD-47 receptor: A molecular modeling study. Arch. Biochem. Biophys 478103-109. (IF= 3.046)

Mouawad L., C. Tetreau, S. Abdel-Azeim, D. Perahia and D. Lavalette.(2007). CO migration pathways in cytochrome P450cam studied by molecular dynamics simulations. Prot. Science 16, 781 (IF= 2.937).

Chapitre de Livre
M. A. Miteva, C. H. Robert, J. D. Marechal, D. Perahia, Receptor Flexibility in Ligand Docking and Virtual Screening" in In silico Lead Discovery,  edited by M. Miteva, Bentham ebooks