Philippe Derreumaux

Philippe Derreumaux

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Philippe Derreumaux

Philippe Derreumaux

Publications by authors named "Philippe Derreumaux"

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100Publications

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Protein-RNA complexation driven by the charge regulation mechanism.

Biochem Biophys Res Commun 2018 Mar 12;498(2):264-273. Epub 2017 Jul 12.

Laboratoire de Cristallographie et RMN Biologiques, UMR 8015 CNRS, Faculté des sciences pharmaceutiques et biologiques, Universtié Paris Descartes et Université Sorbonne Paris Cité, 4 Avenue de l'Observatoire, 75006 Paris, France.

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March 2018

Multi-scale simulations of biological systems using the OPEP coarse-grained model.

Biochem Biophys Res Commun 2018 Mar 14;498(2):296-304. Epub 2017 Sep 14.

Laboratoire de Biochimie Théorique, UPR 9080, CNRS, Université Denis Diderot, Sorbonne Paris Cité, PSL Research University, IBPC, 13 Rue Pierre et Marie Curie, 75005, Paris, France. Electronic address:

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March 2018

Molecular Mechanism of Protein Unfolding under Shear: A Lattice Boltzmann Molecular Dynamics Study.

J Phys Chem B 2018 02 30;122(5):1573-1579. Epub 2018 Jan 30.

ISC-CNR , via dei Taurini, 00185 Rome, Italy.

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February 2018

Influence of electric field on the amyloid-β(29-42) peptides embedded in a membrane bilayer.

J Chem Phys 2018 Jan;148(4):045105

Laboratoire de Biochimie Théorique, Institut de Biologie Physico-Chimique (IBPC), UPR9080 CNRS, Université Paris Diderot, Sorbonne Paris Cité, 13 Rue Pierre et Marie Curie, 75005 Paris, France.

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January 2018

Amyloid-β/Drug Interactions from Computer Simulations and Cell-Based Assays.

J Alzheimers Dis 2018 ;64(s1):S659-S672

Laboratoire de Biochimie Théorique, UPR 9080 CNRS, Université Paris Diderot, Sorbonne Paris Cité, IBPC, Paris, France.

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January 2018

VLITL is a major cross-β-sheet signal for fibrinogen Aα-chain frameshift variants.

Blood 2017 12 31;130(25):2799-2807. Epub 2017 Oct 31.

Institut National de la Santé et de la Recherche Médicale, Unité mixte de Recherche U_1163, Institut IMAGINE, Université Paris Descartes, Sorbonne Paris Cité, Paris, France.

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December 2017

Multifunctional energy landscape for a DNA G-quadruplex: An evolved molecular switch.

J Chem Phys 2017 Oct;147(15):152715

University Chemical Laboratories, Lensfield Road, Cambridge CB2 1EW, United Kingdom.

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October 2017

Why Is Research on Amyloid-β Failing to Give New Drugs for Alzheimer's Disease?

ACS Chem Neurosci 2017 07 6;8(7):1435-1437. Epub 2017 Jun 6.

Laboratoire de Biochimie Théorique, UPR 9080 CNRS, Université Paris Diderot, Sorbonne Paris Cité, IBPC, 13 Rue Pierre et Marie Curie, 75005 Paris, France.

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July 2017

What Can Human-Guided Simulations Bring to RNA Folding?

Biophys J 2017 Jul 22;113(2):302-312. Epub 2017 Jun 22.

Laboratoire de Cristallographie et RMN Biologiques, Université Paris Descartes, Sorbonne Paris Cité, Paris, France. Electronic address:

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July 2017

High-Resolution Structures of the Amyloid-β 1-42 Dimers from the Comparison of Four Atomistic Force Fields.

J Phys Chem B 2017 06 7;121(24):5977-5987. Epub 2017 Jun 7.

Laboratoire de Biochimie Théorique, UPR 9080 CNRS, Université Paris Diderot , Sorbonne Paris Cité, IBPC, 13 Rue Pierre et Marie Curie, 75005 Paris, France.

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June 2017

A Computational Methodology to Overcome the Challenges Associated With the Search for Specific Enzyme Targets to Develop Drugs Against .

Bioinform Biol Insights 2017 12;11:1177932217712471. Epub 2017 Jun 12.

Laboratório de Modelagem de Sistemas Biológicos, Instituto Nacional de Ciência e Tecnologia de Inovação em Doenças de Populações Negligenciadas (INCT-IDPN), Centro de Desenvolvimento Tecnológico em Saúde (CDTS), Fundação Oswaldo Cruz (Fiocruz), Rio de Janeiro, Brazil.

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June 2017

Small static electric field strength promotes aggregation-prone structures in amyloid-β(29-42).

J Chem Phys 2017 Apr;146(14):145101

Laboratoire de Biochimie Theorique, Institut de Biologie Physico-Chimique (IBPC), UPR9080 CNRS, Universite Paris Diderot, Sorbonne Paris Cite, 13 Rue Pierre et Marie Curie, 75005 Paris, France.

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April 2017

Conformational Ensembles of the Wild-Type and S8C Aβ1-42 Dimers.

J Phys Chem B 2017 03 10;121(11):2434-2442. Epub 2017 Mar 10.

Laboratoire de Biochimie Théorique, UPR 9080 CNRS, Université Paris Diderot, Sorbonne Paris Cité, IBPC , 13 Rue Pierre et Marie Curie, 75005 Paris, France.

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March 2017

Fast coarse-grained model for RNA titration.

J Chem Phys 2017 Jan;146(3):035101

Laboratoire de Biochimie Theórique, UPR 9080 CNRS, Institut de Biologie Physico Chimique, Université Paris Diderot - Paris 7 et Université Sorbonne Paris Cité, 13 rue Pierre et Marie Curie, 75005 Paris, France.

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January 2017

Coarse-Grained Simulations Complemented by Atomistic Molecular Dynamics Provide New Insights into Folding and Unfolding of Human Telomeric G-Quadruplexes.

J Chem Theory Comput 2016 Dec 11;12(12):6077-6097. Epub 2016 Nov 11.

Institute of Biophysics, Academy of Sciences of the Czech Republic , Královopolská 135, 612 65 Brno, Czech Republic.

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December 2016

Dimerization Mechanism of Alzheimer Aβ Peptides: The High Content of Intrapeptide-Stabilized Conformations in A2V and A2T Heterozygous Dimers Retards Amyloid Fibril Formation.

J Phys Chem B 2016 12 16;120(47):12111-12126. Epub 2016 Nov 16.

Departament de Fisicoquímica, Facultat de Farmàcia, Universitat de Barcelona , 08028 Barcelona, Catalonia, Spain.

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December 2016

Multiscale simulation of molecular processes in cellular environments.

Philos Trans A Math Phys Eng Sci 2016 Nov;374(2080)

Istituto Sistemi Complessi-ISC, Consiglio Nazionale delle Ricerche, P.za A. Moro 2, 00185 Rome, Italy

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November 2016

Nonequilibrium all-atom molecular dynamics simulation of the bubble cavitation and application to dissociate amyloid fibrils.

J Chem Phys 2016 Nov;145(17):174113

Laboratoire de Biochimie Théorique, UPR 9080, CNRS, Université Denis Diderot, Sorbonne Paris Cité, IBPC, 13 rue Pierre et Marie Curie, 75005 Paris, France.

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November 2016

In silico structural characterization of protein targets for drug development against Trypanosoma cruzi.

J Mol Model 2016 Oct 24;22(10):244. Epub 2016 Sep 24.

Laboratoire de Biochimie Théorique, CNRS UPR 9080, Institut de Biologie Physico - Chimique, Université Paris Diderot, Sorbonne Paris Cité, 75005, Paris, France.

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October 2016

PEP-FOLD3: faster de novo structure prediction for linear peptides in solution and in complex.

Nucleic Acids Res 2016 Jul 29;44(W1):W449-54. Epub 2016 Apr 29.

Molécules Thérapeutiques in Silico, RPBS, INSERM UMR-S 973, Université Paris Diderot, Sorbonne Paris Cité, 75205 Paris Cedex 13, France

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July 2016

Electrostatics analysis of the mutational and pH effects of the N-terminal domain self-association of the major ampullate spidroin.

Soft Matter 2016 Jul 2;12(25):5600-12. Epub 2016 Jun 2.

Departamento de Física e Química, Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Av. do café, s/no. - Universidade de São Paulo, BR-14040-903 Ribeirão Preto - SP, Brazil.

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July 2016

Hydrodynamic effects on β-amyloid (16-22) peptide aggregation.

J Chem Phys 2016 Jul;145(3):035102

Laboratoire de Biochimie Théorique, IBPC, CNRS UPR9080, University Paris Diderot, Sorbonne Paris Cité, 13 rue Pierre et Marie Curie, 75005 Paris, France.

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July 2016

Impact of the A2V Mutation on the Heterozygous and Homozygous Aβ1-40 Dimer Structures from Atomistic Simulations.

ACS Chem Neurosci 2016 06 29;7(6):823-32. Epub 2016 Mar 29.

Laboratoire de Biochimie Théorique, UPR 9080 CNRS, Université Paris Diderot, Sorbonne Paris Cité, IBPC, 13 Rue Pierre et Marie Curie, 75005 Paris, France.

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June 2016

Lattice model for amyloid peptides: OPEP force field parametrization and applications to the nucleus size of Alzheimer's peptides.

J Chem Phys 2016 May;144(20):205103

Laboratoire de Biochimie Théorique, UPR 9080, CNRS, Université Denis Diderot, Sorbonne Paris Cité IBPC, 13 rue Pierre et Marie Curie, 75005 Paris, France.

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May 2016

Picosecond infrared laser-induced all-atom nonequilibrium molecular dynamics simulation of dissociation of viruses.

Phys Chem Chem Phys 2016 04;18(17):11951-8

Laboratoire de Biochimie Theorique, UPR 9080 CNRS, IBPC, Universite Paris 7, 13 rue Pierre et Marie Curie, 75005, Paris, France.

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April 2016

Evaluation of the coarse-grained OPEP force field for protein-protein docking.

BMC Biophys 2016 21;9. Epub 2016 Apr 21.

Institute of Complex Systems: Structural Biochemistry (ICS-6), Forschungszentrum Jülich GmbH, Jülich, 52425 Germany ; Institute of Theoretical and Computational Chemistry, Heinrich Heine University Düsseldorf, Universitätsstr. 1, Düsseldorf, 40225 Germany.

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April 2016

Picosecond melting of peptide nanotubes using an infrared laser: a nonequilibrium simulation study.

Phys Chem Chem Phys 2015 Nov;17(41):27275-80

Department of Physics, North Carolina State University, Raleigh, NC 27695-8202, USA.

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November 2015

Picosecond dissociation of amyloid fibrils with infrared laser: A nonequilibrium simulation study.

J Chem Phys 2015 Oct;143(15):155101

Laboratoire de Biochimie Théorique, UPR 9080, CNRS Université Denis Diderot, Sorbonne Paris Cité IBPC, 13 rue Pierre et Marie Curie, 75005 Paris, France.

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October 2015

Combined experimental and simulation studies suggest a revised mode of action of the anti-Alzheimer disease drug NQ-Trp.

Chemistry 2015 Sep 14;21(36):12657-66. Epub 2015 Jul 14.

CNRS, LCC (Laboratoire de Chimie de Coordination), 205 route de Narbonne, BP 44099, 31077 Toulouse Cedex 4 (France) and Université de Toulouse, UPS, INPT, 31077 Toulouse Cedex 4 (France).

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September 2015

Structures of the Alzheimer's Wild-Type Aβ1-40 Dimer from Atomistic Simulations.

J Phys Chem B 2015 Aug 6;119(33):10478-87. Epub 2015 Aug 6.

Laboratoire de Biochimie Théorique, UPR 9080 CNRS, IBPC, Université Paris Diderot, Sorbonne Paris Cité, 13 Rue Pierre et Marie Curie, 75005 Paris, France.

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August 2015

Communication: Multiple atomistic force fields in a single enhanced sampling simulation.

J Chem Phys 2015 Jul;143(2):021101

Laboratoire de Biochimie Théorique, UPR 9080, CNRS, Université Denis Diderot, Sorbonne Paris Cité IBPC, 13 rue Pierre et Marie Curie, 75005 Paris, France.

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July 2015

Coarse-Grained HiRE-RNA Model for ab Initio RNA Folding beyond Simple Molecules, Including Noncanonical and Multiple Base Pairings.

J Chem Theory Comput 2015 Jul 16;11(7):3510-22. Epub 2015 Jun 16.

Laboratoire de Biochimie Théorique UPR 9080 CNRS, Université Paris Diderot , Sorbonne, Paris Cité, IBPC 13 rue Pierre et Marie Curie, 75005 Paris, France.

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July 2015

Folding Atomistic Proteins in Explicit Solvent Using Simulated Tempering.

J Phys Chem B 2015 Jun 29;119(23):6941-51. Epub 2015 May 29.

†Laboratoire de Biochimie Théorique, UPR 9080 CNRS, Université Denis Diderot, Sorbonne Paris Cité, IBPC, 13 rue Pierre et Marie Curie, 75005 Paris, France.

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June 2015

Ab initio RNA folding.

J Phys Condens Matter 2015 Jun 20;27(23):233102. Epub 2015 May 20.

Laboratoire de Biochimie Théorique UPR 9080 CNRS, Université Paris Diderot, Sorbonne, Paris Cité, IBPC 13 rue Pierre et Marie Curie, 75005 Paris, France.

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June 2015

Epock: rapid analysis of protein pocket dynamics.

Bioinformatics 2015 May 12;31(9):1478-80. Epub 2014 Dec 12.

Laboratoire de Biochimie Théorique, CNRS, UPR9080, Univ Paris Diderot, Sorbonne Paris Cité, F-75005 Paris, France and Structural Bioinformatics and Computational Biochemistry Unit, Department of Biochemistry, University of Oxford, Oxford OX1 3QU, UK.

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May 2015

Protein Simulations in Fluids: Coupling the OPEP Coarse-Grained Force Field with Hydrodynamics.

J Chem Theory Comput 2015 Apr;11(4):1843-53

CNR-IPCF, Consiglio Nazionale delle Ricerche, Rome, Italy.

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April 2015

Molecular structure of the NQTrp inhibitor with the Alzheimer Aβ1-28 monomer.

Eur J Med Chem 2015 Feb 1;91:43-50. Epub 2014 Jul 1.

Laboratoire de Biochimie Théorique, UPR 9080 CNRS, Université Paris Diderot, Sorbonne Paris Cité, IBPC, 13 Rue Pierre et Marie Curie, 75005 Paris, France; Institut Universitaire de France, IUF, 103 Boulevard Saint-Michel, 75005 Paris, France. Electronic address:

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February 2015

Inhibition of protein aggregation and amyloid formation by small molecules.

Curr Opin Struct Biol 2015 Feb 2;30:50-56. Epub 2015 Jan 2.

Laboratoire de Biochimie Théorique, UPR 9080 CNRS, Université Paris Diderot, Sorbonne Paris Cité, IBPC, 13 rue Pierre et Marie Curie, 75005 Paris, France; Institut Universitaire de France, IUF, 103 Boulevard Saint-Michel, 75005 Paris, France. Electronic address:

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February 2015

Are coarse-grained models apt to detect protein thermal stability? The case of OPEP force field.

J Non Cryst Solids 2015 Jan 22;407:494-501. Epub 2014 Jul 22.

Laboratoire de Biochimie Théorique, IBPC, CNRS, UPR9080, Univ. Paris Diderot, Sorbonne Paris Cité, France.

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January 2015

Improved PEP-FOLD Approach for Peptide and Miniprotein Structure Prediction.

J Chem Theory Comput 2014 Oct;10(10):4745-58

INSERM U973 , MTi, F-75205 Paris, France.

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October 2014

Effect of the English familial disease mutation (H6R) on the monomers and dimers of Aβ40 and Aβ42.

ACS Chem Neurosci 2014 Aug 30;5(8):646-57. Epub 2014 Jun 30.

Institute of Physics, Polish Academy of Sciences , Al. Lotnikow 32/46, 02-668 Warsaw, Poland.

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August 2014

The OPEP protein model: from single molecules, amyloid formation, crowding and hydrodynamics to DNA/RNA systems.

Chem Soc Rev 2014 Jul 23;43(13):4871-93. Epub 2014 Apr 23.

Laboratoire de Biochimie Théorique, UPR 9080 CNRS, Université Paris Diderot, Sorbonne Paris Cité, IBPC, 13 rue Pierre et Marie Curie, 75005, Paris, France.

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July 2014

Amyloid oligomer structure characterization from simulations: a general method.

J Chem Phys 2014 Mar;140(9):094105

Laboratoire de Biochimie Théorique, UPR 9080, CNRS Université Denis Diderot, Sorbonne Paris Cité IBPC, 13 rue Pierre et Marie Curie, 75005 Paris, France.

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March 2014

Atomic and dynamic insights into the beneficial effect of the 1,4-naphthoquinon-2-yl-L-tryptophan inhibitor on Alzheimer's Aβ1-42 dimer in terms of aggregation and toxicity.

ACS Chem Neurosci 2014 Feb 22;5(2):148-59. Epub 2013 Nov 22.

Laboratoire de Biochimie Théorique, UPR9080 CNRS, Université Paris Diderot, Sorbonne Paris Cité, Institut de Biologie Physico-Chimique, 13 rue Pierre et Marie Curie, 75005 Paris, France.

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February 2014

Understanding amyloid fibril nucleation and aβ oligomer/drug interactions from computer simulations.

Acc Chem Res 2014 Feb 24;47(2):603-11. Epub 2013 Dec 24.

Laboratoire de Biochimie Théorique, UPR 9080 CNRS, Université Paris Diderot, Sorbonne Paris Cité, IBPC , 13 rue Pierre et Marie Curie, 75005 Paris, France.

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February 2014

Familial Alzheimer A2 V mutation reduces the intrinsic disorder and completely changes the free energy landscape of the Aβ1-28 monomer.

J Phys Chem B 2014 Jan 7;118(2):501-10. Epub 2014 Jan 7.

Laboratoire de Biochimie Théorique, UPR 9080 CNRS, Université Paris Diderot, Sorbonne Paris Cité, IBPC , 13 rue Pierre et Marie Curie, 75005 Paris, France.

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January 2014

Effect of the Tottori familial disease mutation (D7N) on the monomers and dimers of Aβ40 and Aβ42.

ACS Chem Neurosci 2013 Nov 16;4(11):1446-57. Epub 2013 Sep 16.

Institute of Physics, Polish Academy of Sciences , Al. Lotnikow 32/46, 02-668 Warsaw, Poland.

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November 2013

Importance of the ion-pair interactions in the OPEP coarse-grained force field: parametrization and validation.

J Chem Theory Comput 2013 Oct;9(10):4574-4584

Laboratoire de Biochimie Théorique, IBPC, CNRS, UPR9080, Univ. Paris Diderot, Sorbonne Paris Cité, 13 rue Pierre et Marie Curie, 75005, Paris, France ; Institut Universitaire de France, Bvd St Michel, 75005, Paris, France.

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October 2013

Coarse-grained simulations of RNA and DNA duplexes.

J Phys Chem B 2013 Jul 26;117(27):8047-60. Epub 2013 Jun 26.

Laboratoire de Biochimie Théorique UPR 9080 CNRS, Université Paris Diderot, Sorbonne, Paris Citè, IBPC 13 rue Pierre et Marie Curie, 75005 Paris, France.

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July 2013

Conformational ensemble and polymorphism of the all-atom Alzheimer's Aβ(37-42) amyloid peptide oligomers.

J Phys Chem B 2013 May 6;117(19):5831-40. Epub 2013 May 6.

Laboratoire de Biochimie Théorique, UPR 9080, CNRS, Université Denis Diderot, Sorbonne Paris Cité, IBPC, 13 rue Pierre et Marie Curie, 75005 Paris, France.

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May 2013

Molecular mechanism of the inhibition of EGCG on the Alzheimer Aβ(1-42) dimer.

J Phys Chem B 2013 Apr 9;117(15):3993-4002. Epub 2013 Apr 9.

School of Biological Sciences, Nanyang Technological University, 60 Nanyang Drive, Singapore 637551.

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April 2013

Coarse-grained models for protein folding and aggregation.

Methods Mol Biol 2013 ;924:585-600

Laboratory of Theoretical Biochemistry, Paris 7 University, Paris, France.

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February 2013

Density functional conformational study of 2-O-sulfated 3,6 anhydro-α-D-galactose and of neo-κ- and ι-carrabiose molecules in gas phase and water.

J Mol Model 2013 Feb 20;19(2):893-904. Epub 2012 Oct 20.

L2MSM, Faculté des Sciences, Université Djillali Liabes de Sidi Bel Abbes, B.P. 89, 22000, Sidi Bel Abbes, Algeria.

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February 2013

Communication: Simulated tempering with fast on-the-fly weight determination.

J Chem Phys 2013 Feb;138(6):061102

Laboratoire de Biochimie Théorique, UPR 9080, CNRS Université Denis Diderot, Sorbonne Paris Cité IBPC, 13 rue Pierre et Marie Curie, 75005 Paris, France.

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February 2013

The coarse-grained OPEP force field for non-amyloid and amyloid proteins.

J Phys Chem B 2012 Aug 16;116(30):8741-52. Epub 2012 Jul 16.

Laboratoire de Biochimie Théorique, CNRS UPR 9080, Université Paris Diderot, Sorbonne Paris Cité, Institut de Biologie Physico-Chimique, 13 rue Pierre et Marie Curie, 75005 Paris.

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August 2012

Structures of Aβ17-42 trimers in isolation and with five small-molecule drugs using a hierarchical computational procedure.

J Phys Chem B 2012 Jul 10;116(29):8412-22. Epub 2012 Feb 10.

Laboratoire de Biochimie Théorique, UPR9080 CNRS, Université Paris Diderot, Sorbonne Paris Cité, Institut de Biologie Physico-Chimique, 13 rue Pierre et Marie Curie, 75005 Paris, France.

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July 2012

Structural, thermodynamical, and dynamical properties of oligomers formed by the amyloid NNQQ peptide: insights from coarse-grained simulations.

J Chem Phys 2012 Jul;137(2):025101

State Key Laboratory of Surface Physics, and Department of Physics, Fudan University, 220 Handan Road, Shanghai 200433, China.

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July 2012

Distinct dimerization for various alloforms of the amyloid-beta protein: Aβ(1-40), Aβ(1-42), and Aβ(1-40)(D23N).

J Phys Chem B 2012 Apr 26;116(13):4043-55. Epub 2012 Mar 26.

Département de Physique and Groupe de recherche sur les protéines membranaires (GEPROM), Université de Montréal, Montréal, Québec, Canada.

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April 2012

Intrinsic determinants of Aβ(12-24) pH-dependent self-assembly revealed by combined computational and experimental studies.

PLoS One 2011 21;6(9):e24329. Epub 2011 Sep 21.

State Key Laboratory of Precision Spectroscopy, Institute of Theoretical and Computational Science, East China Normal University, Shanghai, China.

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February 2012

Flexibility and binding affinity in protein-ligand, protein-protein and multi-component protein interactions: limitations of current computational approaches.

J R Soc Interface 2012 Jan 12;9(66):20-33. Epub 2011 Oct 12.

INSERM UMR-S 973, Université Paris Diderot, 35 rue Hélène Brion, 75251 Paris cedex, France.

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January 2012

Configurational entropy: an improvement of the quasiharmonic approximation using configurational temperature.

Phys Chem Chem Phys 2012 Jan 25;14(2):877-86. Epub 2011 Nov 25.

Laboratoire de Biochimie Théorique, CNRS, UPR9080, Université Paris Diderot, Sorbonne Paris Cité, Institut de Biologie Physico-Chimique, Paris, France.

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January 2012

Carbon nanotube inhibits the formation of β-sheet-rich oligomers of the Alzheimer's amyloid-β(16-22) peptide.

Biophys J 2011 Nov 1;101(9):2267-76. Epub 2011 Nov 1.

State Key Laboratory of Surface Physics and Department of Physics, Fudan University, Shanghai, China.

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November 2011

Distinct Morphologies for Amyloid Beta Protein Monomer: Aβ1-40, Aβ1-42, and Aβ1-40(D23N).

J Chem Theory Comput 2011 Aug 29;7(8):2584-92. Epub 2011 Jun 29.

Département de Physique and Groupe de Recherche Sur Les Protéines Membranaires (GEPROM), Université de Montréal , C.P. 6128, succursale Centre-ville, Montréal (Québec), Canada.

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August 2011

Assessing the Quality of the OPEP Coarse-Grained Force Field.

J Chem Theory Comput 2011 Jun 19;7(6):1928-34. Epub 2011 May 19.

Laboratoire de Biochimie Théorique, UPR 9080 CNRS, Institut de Biologie Physico-Chimique and Université Paris Diderot, Paris 7, Institut Universitaire de France , 13 rue Pierre et Marie Curie, 75005 Paris, France.

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June 2011

Effects of all-atom force fields on amyloid oligomerization: replica exchange molecular dynamics simulations of the Aβ(16-22) dimer and trimer.

Phys Chem Chem Phys 2011 May 12;13(20):9778-88. Epub 2011 Apr 12.

Institute of Physical and Theoretical Chemistry, Goethe University, Max-von-Laue-Str. 7, D-60438 Frankfurt, Germany.

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May 2011

Impact of Thermostats on Folding and Aggregation Properties of Peptides Using the Optimized Potential for Efficient Structure Prediction Coarse-Grained Model.

J Chem Theory Comput 2011 May 11;7(5):1502-10. Epub 2011 Apr 11.

Laboratoire de Biochimie Théorique, UPR 9080 CNRS et Université Paris Diderot (Paris 7), Institut de Biologie Physico Chimique , 13 rue Pierre et Marie Curie, 75005 Paris, France.

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May 2011

A multiscale approach to characterize the early aggregation steps of the amyloid-forming peptide GNNQQNY from the yeast prion sup-35.

PLoS Comput Biol 2011 May 19;7(5):e1002051. Epub 2011 May 19.

Département de Physique and GEPROM, Université de Montréal, Montréal, Québec, Canada.

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May 2011

Effects of G33A and G33I mutations on the structures of monomer and dimer of the amyloid-β fragment 29-42 by replica exchange molecular dynamics simulations.

J Phys Chem B 2011 Feb 27;115(5):1282-8. Epub 2010 Dec 27.

State Key Laboratory of Surface Physics, Department of Physics, Fudan University, Shanghai, China.

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February 2011

HiRE-RNA: a high resolution coarse-grained energy model for RNA.

J Phys Chem B 2010 Sep;114(37):11957-66

Laboratoire de Biochimie Théorique, UPR 9080 CNRS, Institut de Biologie Physico Chimique et Université Paris Diderot-Paris 7, 13 rue Pierre et Marie Curie, 75005 Paris, France.

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September 2010

Low molecular weight oligomers of amyloid peptides display beta-barrel conformations: a replica exchange molecular dynamics study in explicit solvent.

J Chem Phys 2010 Apr;132(16):165103

Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom.

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April 2010

A fast method for large-scale de novo peptide and miniprotein structure prediction.

J Comput Chem 2010 Mar;31(4):726-38

MTi, INSERM UMR-S973 and RPBS, Université Paris Diderot - Paris 7, 5 rue Marie-Andrée Lagroua Weill-Halle, 75205 Paris, Cedex 13, France.

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March 2010

Effects of the RGTFEGKF inhibitor on the structures of the transmembrane fragment 70-86 of glycophorin A: an all-atom molecular dynamics study.

J Phys Chem B 2010 Jan;114(2):1004-9

Surface Physics Laboratory (National Key Laboratory) and Department of Physics, Fudan University, 220 Handan Road, Shanghai, 200433, People's Republic of China.

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January 2010

Induced beta-barrel formation of the Alzheimer's Abeta25-35 oligomers on carbon nanotube surfaces: implication for amyloid fibril inhibition.

Biophys J 2009 Sep;97(6):1795-803

Surface Physics Laboratory and Department of Physics, Fudan University, Shanghai, China.

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September 2009

PEP-FOLD: an online resource for de novo peptide structure prediction.

Nucleic Acids Res 2009 Jul 11;37(Web Server issue):W498-503. Epub 2009 May 11.

MTi, INSERM UMR-S 973, - Paris 7, 35 rue H. Brion, F75205, Paris, France.

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July 2009

Energy flow and long-range correlations in guanine-binding riboswitch: a nonequilibrium molecular dynamics study.

J Phys Chem B 2009 Jul;113(27):9340-7

Institute of Physical and Theoretical Chemistry, Goethe University, Max-von-Laue-Strasse 7, D-60438 Frankfurt, Germany.

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July 2009

Thermodynamics and dynamics of amyloid peptide oligomerization are sequence dependent.

Proteins 2009 Jun;75(4):954-63

Department of Physics and National Key Surface Physics Laboratory, Fudan University, 220 Handan Road, Shanghai, 200433, China.

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June 2009

Targeting the early steps of Abeta16-22 protofibril disassembly by N-methylated inhibitors: a numerical study.

Proteins 2009 May;75(2):442-52

Laboratoire de Biochimie Théorique, UPR 9080 CNRS, Institut de Biologie, Physico Chimique et Université Paris 7 Denis Diderot, 13 rue Pierre et Marie Curie, Paris 75005, France.

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May 2009

The conversion of helix H2 to beta-sheet is accelerated in the monomer and dimer of the prion protein upon T183A mutation.

J Phys Chem B 2009 May;113(19):6942-8

Laboratoire de Biochimie Theorique, UPR 9080 CNRS, Institut de Biologie Physico Chimique et Universite Paris Diderot-Paris 7, 13 rue Pierre et Marie Curie, 75005 Paris, France.

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May 2009

Structures and thermodynamics of Alzheimer's amyloid-beta Abeta(16-35) monomer and dimer by replica exchange molecular dynamics simulations: implication for full-length Abeta fibrillation.

J Phys Chem B 2009 May;113(21):7668-75

Laboratoire de Biochimie Théeorique, UPR 9080 CNRS, Institut de Biologie Physico Chimique et Université Paris Diderot-Paris 7, 13 rue Pierre et Marie Curie, 75005 Paris, France.

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May 2009

Computational simulations of the early steps of protein aggregation.

Prion 2007 Jan-Mar;1(1):3-8. Epub 2007 Jan 5.

Department of Physics, Fudan University, Shanghai, China.

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March 2009

Structural diversity of the soluble trimers of the human amylin(20-29) peptide revealed by molecular dynamics simulations.

J Chem Phys 2009 Mar;130(12):125101

Department of Physics and Surface Physics Laboratory, Fudan University, 220 Handan Road, Shanghai 200433, China.

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March 2009

Replica exchange molecular dynamics simulations of coarse-grained proteins in implicit solvent.

J Phys Chem B 2009 Jan;113(1):267-74

Institut de Biologie Physico-Chimique et Universite Paris 7 Denis Diderot, 75005 Paris, France.

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January 2009

The beta-strand-loop-beta-strand conformation is marginally populated in beta2-microglobulin (20-41) peptide in solution as revealed by replica exchange molecular dynamics simulations.

Biophys J 2008 Jul 11;95(2):510-7. Epub 2008 Apr 11.

National Key Surface Physics Laboratory and Department of Physics, Fudan University, Shanghai, China.

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July 2008

Role of the region 23-28 in Abeta fibril formation: insights from simulations of the monomers and dimers of Alzheimer's peptides Abeta40 and Abeta42.

Curr Alzheimer Res 2008 Jun;5(3):244-50

Laboratoire de Biochimie Théorique, UPR9080 CNRS, Institut de Biologie Physico-Chimique et Université Paris 7 Denis-Diderot, Paris, France.

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June 2008

Exploring energy landscapes of protein folding and aggregation.

Front Biosci 2008 May 1;13:4495-516. Epub 2008 May 1.

Departement de physique, Universite de Montreal, Case postale 6128, succursale centre-ville, Montreal, (Quebec), Canada H3C 3J7.

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May 2008

Self-assembly of amyloid-forming peptides by molecular dynamics simulations.

Front Biosci 2008 May 1;13:5681-92. Epub 2008 May 1.

National Key Surface Physics Laboratory and Department of Physics, Fudan University, Shanghai 200433, China.

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May 2008

Self-assembly of the beta2-microglobulin NHVTLSQ peptide using a coarse-grained protein model reveals a beta-barrel species.

J Phys Chem B 2008 Apr 15;112(14):4410-8. Epub 2008 Mar 15.

Department of Physics, Fudan University, Shanghai 200433, China.

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April 2008

Energy landscapes of the monomer and dimer of the Alzheimer's peptide Abeta(1-28).

J Chem Phys 2008 Mar;128(12):125108

Département de Physique and Regroupement Québécois sur les Matériaux de Pointe, Université de Montréal, C.P. 6128, Succursale Centre-Ville, Montréal, Québec H3C 3J7, Canada.

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March 2008

The complex folding pathways of protein A suggest a multiple-funnelled energy landscape.

J Chem Phys 2008 Jan;128(4):045101

Département de Physique, Université de Montréal, C.P. 6128, Succursale Centre-Ville, Montréal, Québec H3C 3J7, Canada.

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January 2008

A coarse-grained protein force field for folding and structure prediction.

Proteins 2007 Nov;69(2):394-408

Equipe de Bioinformatique Génomique et Moléculaire, INSERM E0346, Université Paris 7, Tour 53-54, 2 place Jussieu, 75251 Paris, Cedex 05, France.

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November 2007

Structure and aggregation mechanism of beta(2)-microglobulin (83-99) peptides studied by molecular dynamics simulations.

Biophys J 2007 Nov 10;93(10):3353-62. Epub 2007 Aug 10.

National Key Surface Physics Laboratory and Department of Physics, Fudan University, Shanghai, China.

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November 2007

Structural and hydration properties of the partially unfolded states of the prion protein.

Biophys J 2007 Aug 4;93(4):1284-92. Epub 2007 May 4.

Dipartimento delle Scienze Biologiche, Sezione Biostrutture and CNISM, Università di Napoli Federico II, I-80134 Naples, Italy.

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August 2007

Probing amyloid fibril formation of the NFGAIL peptide by computer simulations.

J Chem Phys 2007 Feb;126(6):065101

Laboratoire de Biochimie Théorique, UPR 9080 CNRS, Institut de Biologie Physico-Chimique et Université Paris 7, 13 rue Pierre et Marie Curie, 75005 Paris, France.

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February 2007

Coarse-grained protein molecular dynamics simulations.

J Chem Phys 2007 Jan;126(2):025101

Laboratoire de Biochimie Théorique, UPR 9080 CNRS, Institut de Biologie Physico, Chimique et Université Paris 7, 13 Rue Pierre et Marie Curie, 75005 Paris, France.

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January 2007

Aggregating the amyloid Abeta(11-25) peptide into a four-stranded beta-sheet structure.

Proteins 2006 Dec;65(4):877-88

Département de Physique and Centre Robert-Cedergren en bioinformatique, Université de Montréal, C.P. 6128, Succursale Centre-ville Montréal, Québec H3C 3J7, Canada.

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December 2006