Philippe Derreumaux

发表

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

Pierre Tufféry, Julien Maupetit, Philippe Derreumaux, 2009, Nucleic Acids Res..

Advancing Multi-Scale Simulation Methods for Biological Membrane Systems

Marc Baaden, Simone Melchionna, Fabio Sterpone, 2019 .

PEP-FOLD: an updated de novo structure prediction server for both linear and disulfide bonded cyclic peptides

Pierre Tufféry, Pierre Thévenet, Frédéric Guyon, 2012, Nucleic Acids Res..

Predicting helical hairpins from sequences by Monte Carlo simulations

Philippe Derreumaux, P. Derreumaux, 2000, J. Comput. Chem..

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

Pierre Tufféry, Julien Rey, Marek Vavrusa, 2016, Nucleic Acids Res..

A truncated Newton minimizer adapted for CHARMM and biomolecular applications

Tamar Schlick, Bernard R. Brooks, Philippe Derreumaux, 1994, J. Comput. Chem..

Epock: rapid analysis of protein pocket dynamics

Matthieu Chavent, Marc Baaden, Mark S. P. Sansom, 2014, Bioinform..

UnityMol: interactive and ludic visual manipulation of coarse-grained RNA and other biomolecules

Marc Baaden, Samuela Pasquali, Antoine Taly, 2015, 2015 IEEE 1st International Workshop on Virtual and Augmented Reality for Molecular Science (VARMS@IEEEVR).

Ab initio RNA folding

Samuela Pasquali, Philippe Derreumaux, Tristan Cragnolini, 2014, Journal of physics. Condensed matter : an Institute of Physics journal.

Impact of the Astaxanthin, Betanin, and EGCG Compounds on Small Oligomers of Amyloid Aβ40 Peptide

James Chapman, Philippe Derreumaux, Vi Khanh Truong, 2020, J. Chem. Inf. Model..

A fast method for large‐scale De Novo peptide and miniprotein structure prediction

Pierre Tufféry, Julien Maupetit, Philippe Derreumaux, 2009, J. Comput. Chem..

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

Philippe Derreumaux, Birgit Strodel, Philipp Kynast, 2016, BMC biophysics.

Mesoscale biosimulations within a unified framework: from proteins to plasmids

Simone Melchionna, Fabio Sterpone, Philippe Derreumaux, 2019, Molecular Simulation.

Improved greedy algorithm for protein structure reconstruction

Pierre Tufféry, Frédéric Guyon, Philippe Derreumaux, 2005, J. Comput. Chem..

UnityMol: Interactive scientific visualization for integrative biology

Marc Baaden, Samuela Pasquali, Philippe Derreumaux, 2014, 2014 IEEE 4th Symposium on Large Data Analysis and Visualization (LDAV).

Dependency between consecutive local conformations helps assemble protein structures from secondary structures using Go potential and greedy algorithm

Philippe Derreumaux, Pierre Tuffery, P. Derreumaux, 2005, Proteins.

What Can Human-Guided Simulations Bring to RNA Folding?

Marc Baaden, Samuela Pasquali, Antoine Taly, 2017, Biophysical journal.

A Multiscale Approach to Characterize the Early Aggregation Steps of the Amyloid-Forming Peptide GNNQQNY from the Yeast Prion Sup-35

Normand Mousseau, Philippe Derreumaux, Jessica Nasica-Labouze, 2011, PLoS Comput. Biol..

Predicting helical hairpins from sequences by Monte Carlo simulations

Philippe Derreumaux, 2000, J. Comput. Chem..

Vibrational molecular force field of model compounds with biologic interest. II. Harmonic dynamics of both anomers of glucose in the crystalline state

Manuel Dauchez, Philippe Derreumaux, Gérard Vergoten, 1993, J. Comput. Chem..

A vibrational molecular force field of model compounds with biological interest. IV. Parameters for the different glycosidic linkages of oligosaccharides

Manuel Dauchez, Philippe Derreumaux, Gérard Vergoten, 1995, J. Comput. Chem..

Conformational studies of neuroactive ligands. 1. Force field and vibrational spectra of crystalline acetylcholine

Warner L. Peticolas, Philippe Derreumaux, K. Jeff Wilson, 1989 .

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

Samuela Pasquali, Philippe Derreumaux, Tristan Cragnolini, 2015, Journal of chemical theory and computation.

Coarse-grained protein molecular dynamics simulations.

Normand Mousseau, Philippe Derreumaux, N. Mousseau, 2007, The Journal of chemical physics.

A new spectroscopic molecular mechanics force field. Parameters for proteins

Philippe Derreumaux, Gérard Vergoten, P. Derreumaux, 1995 .

Role of supersecondary structural elements in protein G folding

Philippe Derreumaux, P. Derreumaux, 2003 .

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

Philippe Derreumaux, Viet Hoang Man, P. Derreumaux, 2017, The journal of physical chemistry. B.

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

Marc Baaden, Samuela Pasquali, Maria Kalimeri, 2014, Chemical Society reviews.

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

Philippe Derreumaux, Pierre Tuffery, P. Derreumaux, 2012, Journal of The Royal Society Interface.

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

Simone Melchionna, Fabio Sterpone, Philippe Derreumaux, 2016, The Journal of chemical physics.

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.

Philippe Derreumaux, Guanghong Wei, Guanghong Wei, 2011, The journal of physical chemistry. B.

Conformational studies of neuroactive ligands. 2. Solution-state conformations of acetylcholine

Warner L. Peticolas, Philippe Derreumaux, K. Jeff Wilson, 1989 .

Finding the low-energy forms of avian pancreatic polypeptide with the diffusion-process-controlled Monte Carlo method

Philippe Derreumaux, P. Derreumaux, 1998 .

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

Samuela Pasquali, David J Wales, Philippe Derreumaux, 2017, The Journal of chemical physics.

Multilevel Lattice Boltzmann-Particle Dynamics simulations at the Physics-Biology interface

Massimo Bernaschi, Sauro Succi, Simone Melchionna, 2017, Journal of Physics: Conference Series.

Sampling the complex energy landscape of a simple β-hairpin

Normand Mousseau, Philippe Derreumaux, Guanghong Wei, 2003 .

Structural characterization of VGVAPG, an elastin-derived peptide.

Manuel Dauchez, Philippe Derreumaux, Nicolas Floquet, 2004, Biopolymers.

Influence of the spectroscopic potential energy function spasiba on molecular dynamics of proteins: comparison with the amber potential

Philippe Derreumaux, Gérard Vergoten, P. Derreumaux, 1993 .

Long timestep dynamics of peptides by the dynamics driver approach

Tamar Schlick, Philippe Derreumaux, T. Schlick, 1995, Proteins.

A diffusion process-controlled Monte Carlo method for finding the global energy minimum of a polypeptide chain. I. Formulation and test on a hexadecapeptide

Philippe Derreumaux, P. Derreumaux, 1997 .

Thermodynamics and dynamics of amyloid peptide oligomerization are sequence dependent

Normand Mousseau, Philippe Derreumaux, Guanghong Wei, 2009, Proteins.

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

Yuko Okamoto, Philippe Derreumaux, Y. Okamoto, 2013, The Journal of chemical physics.

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

Mai Suan Li, Philippe Derreumaux, P. Derreumaux, 2011, Physical chemistry chemical physics : PCCP.

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

Massimiliano Bonomi, Alessandro Barducci, Philippe Derreumaux, 2011, Journal of chemical theory and computation.

Coarse‐grained and All‐atom Simulations towards the Early and Late Steps of Amyloid Fibril Formation

Simone Melchionna, Fabio Sterpone, Philippe Derreumaux, 2017 .

Modelling lipid systems in fluid with Lattice Boltzmann Molecular Dynamics simulations and hydrodynamics

Marc Baaden, Simone Melchionna, Fabio Sterpone, 2019, Scientific Reports.

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

Philippe Derreumaux, Guanghong Wei, Guanghong Wei, 2012, The Journal of chemical physics.

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

Samuela Pasquali, Philippe Derreumaux, Yassmine Chebaro, 2012, The journal of physical chemistry. B.

Normal‐coordinate treatment of a nucleic base pair model in its crystalline state: 1‐Methylcytosine–9‐ethylguanine

Philippe Derreumaux, Gérard Vergoten, P. Derreumaux, 1990 .

THE OPEP COARSE-GRAINED PROTEIN MODEL: FROM SINGLE MOLECULES, AMYLOID FORMATION, ROLE OF MACROMOLECULAR CROWDING AND HYDRODYNAMICS TO RNA/DNA COMPLEXES

Marc Baaden, Samuela Pasquali, Maria Kalimeri, 2014 .

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

Philippe Derreumaux, P. Derreumaux, P. Nguyen, 2016, The Journal of chemical physics.

Folding Atomistic Proteins in Explicit Solvent Using Simulated Tempering.

Yuguang Mu, Philippe Derreumaux, Jessica Nasica-Labouze, 2015, The journal of physical chemistry. B.

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

Philippe Derreumaux, P. Derreumaux, P. Nguyen, 2012, Physical chemistry chemical physics : PCCP.

Effect of urey–bradley–shimanouchi force field on the harmonic dynamics of proteins

Philippe Derreumaux, P. Derreumaux, Géarard Vergoten, 1991, Proteins.

Multiscale simulation of molecular processes in cellular environments

Simone Melchionna, Fabio Sterpone, Philippe Derreumaux, 2016, Philosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences.

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

Normand Mousseau, Philippe Derreumaux, Sébastien Côté, 2012, The journal of physical chemistry. B.

Exploring the energy landscape of proteins: A characterization of the activation-relaxation technique

Normand Mousseau, Philippe Derreumaux, Guanghong Wei, 2002 .

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

Phuong Nguyen, Philippe Derreumaux, P. Derreumaux, 2014, Accounts of chemical research.