2017

Conformational polymorphism or structural invariance in DNA photoinduced lesions: implications for repair rates
Francois Dehez; Hugo Gattuso; Emmanuelle Bignon; Christophe Morell; Elise Dumont; Antonio Monari;
Nucleic Acids Research (2017) 45 (7): 3654-3662


Deciphering the photosensitization mechanisms of hypericin towards biological membranes
Hugo Gattuso; Marco Marazzi; Francois Dehez; Antonio Monari;
Phys. Chem. Chem. Phys. (2017) 57 (34): 149-23193


Effect of Meso vs Macro Size of Hierarchical Porous Silica on the Adsorption and Activity of Immobilized β-Galactosidase
Ileana-Alexandra Pavel; Sofia F. Prazeres; Gemma Montalvo; Carmen Garc; ıa Ruiz; Vincent Nicolas; Alain Celzard; Francois Dehez; Laetitia Canabady-Rochelle; Nadia Canilho; Andreea Pasc;
Langmuir (2017) 33 (13): 3333-3340


Structural and energetic study of cation–π–cation interactions in proteins
Silvana Pinheiro; Ignacio Soteras; Josep Lluis Gelpi; Francois Dehez; Christophe Chipot; F. Javier Luque; Carles Curutchet;
Phys. Chem. Chem. Phys. (2017) 15 (15): 686-9861


Permeability of a Fluid Lipid Bilayer to Short-Chain Alcohols from First Principles
Jeffrey Comer; Klaus Schulten; Christophe Chipot;
Journal of Chemical Theory and Computation (2017) 13 (6): 2523-2532


Methodology for the Simulation of Molecular Motors at Different Scales
Abhishek Singharoy; Christophe Chipot;
The Journal of Physical Chemistry B (2017) 121 (15): 3502-3514


Chemomechanical Coupling in Hexameric Protein–Protein Interfaces Harnesses Energy within V-Type ATPases
Abhishek Singharoy; Christophe Chipot; Mahmoud Moradi; Klaus Schulten;
Journal of the American Chemical Society (2017) 139 (1): 293-310


Foscholine detergents for biophysical studies of membrane proteins: an emerging consensus on strengths and weaknesses
C. Chipot, F. Dehez, J. R. Schnell, N. Zitzmann, E. Pebay-Peyroula, L. Catoire, B. Miroux, E. R. S. Kunji, G. Veglia, T. A. Cross, P. Schanda
Chemical Review, 2017, submitted


Hepatitis C virus sequence divergence preserves p7 protein structural and dynamic features
B. Oestringer , J. Bolivar ,J. Claridge , L. Almanea , C. Chipot , F. Dehez , N. Holzmann , J. Schnell
Scientific Reports, 2017, in revision


Viroporin p7 falls apart in DPC detergent
D. Oestringer , J. Bolivar , J. Claridge , C. Chipot , F. Dehez , N. Holzmann , N. Zitzmann , J. Schnell
Nature, 2017, submitted


Dynamics and interactions of ADP/ATP transporter AAC3 in DPC detergent are not functionally relevant
V. Kurauskas , A. Hessel , F. Dehez , C. Chipot , B. Bersch, P. Schanda
Nature Structural Biology, 2017, in revision


How detergent impacts membrane proteins: the case of mitochondrial carriers in dodecylphosphocholine
V. Kurauskas , A. Hessel , P. Ma, , P. Lunetti, L. Imbert, M. S. King, R. Sounier, V. Dolce, E. R. S. Kunji, L. Capobianco, C. Chipot , F. Dehez, B. Bersch, P. Schanda
eLife, 2017, submitted


Cardiolipins bound to the mitochondrial ADP/ATP carrier in dodecylphosphocholine have disordered acyl chains and a non-native affinity
F. Dehez, P. Schanda, M. S. King, E. R. S. Kunji, C. Chipot
Biophysical Journal, 2017, in revision


Tribute to Klaus Schulten
Emad Tajkhorshid; Christophe Chipot;
The Journal of Physical Chemistry B (2017) 121 (15): 3203-3205


The Extended Generalized Adaptive Biasing Force Algorithm for Multidimensional Free-Energy Calculations
Tanfeng Zhao; Haohao Fu; Tony Lelievre; Xueguang Shao; Christophe Chipot; Wensheng Cai;
Journal of Chemical Theory and Computation (2017) 13 (4): 1566-1576


The lubricating role of water in the shuttling of rotaxanes
Haohao Fu; Xueguang Shao; Christophe Chipot; Wensheng Cai;
Chem. Sci. (2017) 139 (7): 293-5094


2016

The true nature of rotary movements in rotaxanes
Peng Liu; Xueguang Shao; Christophe Chipot; Wensheng Cai;
Chem. Sci. (2016) 9 (1): 18-462


High-speed atomic force microscopy shows that annexin V stabilizes membranes on the second timescale
Atsushi Miyagi; Christophe Chipot; Martina Rangl; Simon Scheuring;
Nature Nanotechnology (2016) 13 (9): 952-790


Molecular Mechanism of Processive 3′ to 5′ RNA Translocation in the Active Subunit of the RNA Exosome Complex
Lela Vukovic; Christophe Chipot; Debora L. Makino; Elena Conti; Klaus Schulten;
Journal of the American Chemical Society (2016) 138 (12): 4069-4078


Decrypting protein insertion through the translocon with free-energy calculations
James C. Gumbart; Christophe Chipot;
Biochimica et Biophysica Acta (BBA) - Biomembranes (2016) 1858 (7): 1663-1671


How Does the Solvent Modulate Shuttling in a Pillararene/Imidazolium [2]Rotaxane? Insights from Free Energy Calculations
Ying Liu; Christophe Chipot; Xueguang Shao; Wensheng Cai;
The Journal of Physical Chemistry C (2016) 120 (11): 6287-6293


Extended Adaptive Biasing Force Algorithm. An On-the-Fly Implementation for Accurate Free-Energy Calculations
Haohao Fu; Xueguang Shao; Christophe Chipot; Wensheng Cai;
Journal of Chemical Theory and Computation (2016) 12 (8): 3506-3513


Simulation-Based Approaches for Determining Membrane Permeability of Small Compounds
Christopher T. Lee; Jeffrey Comer; Conner Herndon; Nelson Leung; Anna Pavlova; Robert V. Swift; Chris Tung; Christopher N. Rowley; Rommie E. Amaro; Christophe Chipot; Yi Wang; James C. Gumbart;
Journal of Chemical Information and Modeling (2016) 56 (4): 721-733


AlaScan: A Graphical User Interface for Alanine Scanning Free-Energy Calculations
Vijayaraj Ramadoss; Francois Dehez; Christophe Chipot;
Journal of Chemical Information and Modeling (2016) 56 (6): 1122-1126


Conserved methionine dictates substrate preference in Nramp-family divalent metal transporters
Aaron T. Bozzi; Lukas B. Bane; Wilhelm A. Weihofen; Anne L. McCabe; Abhishek Singharoy; Christophe J. Chipot; Klaus Schulten; Rachelle Gaudet;
Proceedings of the National Academy of Sciences (2016) 118 (16): 4351-10315


Leveraging the Information from Markov State Models To Improve the Convergence of Umbrella Sampling Simulations
Sunhwan Jo; Donghyuk Suh; Ziwei He; Christophe Chipot; Benoit Roux;
The Journal of Physical Chemistry B (2016) 120 (33): 8733-8742


Assessing the physiological relevance of alternate architectures of the p7 protein of hepatitis C virus in different environments
Nicole Holzmann; Christophe Chipot; Francois Penin; Francois Dehez;
Medicinal Chemistry (2016) 24 (20): 4920-4927


Repair Rate of Clustered Abasic DNA Lesions by Human Endonuclease: Molecular Bases of Sequence Specificity
Hugo Gattuso; Elodie Durand; Emmanuelle Bignon; Christophe Morell; Alexandros G. Georgakilas; Elise Dumont; Christophe Chipot; Francois Dehez; Antonio Monari;
The Journal of Physical Chemistry Letters (2016) 7 (19): 3760-3765


Complex Movements in Rotaxanes: Shuttling Coupled with Conformational Transition of Cyclodextrins
Shuangshuang Wang; Tanfeng Zhao; Xueguang Shao; Christophe Chipot; Wensheng Cai;
The Journal of Physical Chemistry C (2016) 120 (34): 19479-19486


Correlation of bistranded clustered abasic DNA lesion processing with structural and dynamic DNA helix distortion
Emmanuelle Bignon; Hugo Gattuso; Christophe Morell; Francois Dehez; Alexandros G. Georgakilas; Antonio Monari; Elise Dumont;
Nucleic Acids Research (2016) 44 (18): 8588-8599


2015

From Molecules to Living Organisms: An Interplay Between Biology and Physics - Editors : Pebay-Peyroula, E.; Nury, H.; Parcy, F.; Ruigrok, R. W. H.; Ziegler, C.; Cugliandolo, L. F.
Dehez, F. (Book Chapter)
Oxford University Press (2015) ISBN : 978-0-19-875295-0


Sonoporation at Small and Large Length Scales: Effect of Cavitation Bubble Collapse on Membranes
Haohao Fu; Jeffrey Comer; Wensheng Cai; Christophe Chipot;
The Journal of Physical Chemistry Letters (2015) 6 (3): 413-418


The Adaptive Biasing Force Method: Everything You Always Wanted To Know but Were Afraid To Ask
Jeffrey Comer; James C. Gumbart; Jerome Henin; Tony Lelievre; Andrew Pohorille; Christophe Chipot;
The Journal of Physical Chemistry B (2015) 119 (3): 1129-1151


Efficient Determination of Relative Entropy Using Combined Temperature and Hamiltonian Replica-Exchange Molecular Dynamics
Sunhwan Jo; Christophe Chipot; Benoit Roux;
Journal of Chemical Theory and Computation (2015) 11 (5): 2234-2244


What causes tumbling of altro-α-CD derivatives? Insight from computer simulations
Ying Liu; Christophe Chipot; Xueguang Shao; Wensheng Cai;
RSC Adv. (2015) 9 (71): 18-57317


Why do the structural properties of complexes formed by glucans and carbon nanotubes differ so much?
Haohao Fu; Christophe Chipot; Xueguang Shao; Wensheng Cai;
RSC Adv. (2015) 10 (116): 5276-95689


2014

Dynamiques molculaires quantiques et classiques
Marquardt, R.; Hnin, J.; Dehez, F.; Chipot, C.
L Actualité Chimique (2014) 382-383 56-62


Achieving ergodic sampling using replica-exchange free-energy calculations
Jeffrey Comer; Benoit Roux; Christophe Chipot;
Molecular Simulation (2014) 31 (1-3): 671-228


Calculation of Lipid-Bilayer Permeabilities Using an Average Force
Jeffrey Comer; Klaus Schulten; Christophe Chipot;
Journal of Chemical Theory and Computation (2014) 10 (2): 554-564


Thermodynamics of Deca-alanine Folding in Water
Anthony Hazel; Christophe Chipot; James C. Gumbart;
Journal of Chemical Theory and Computation (2014) 10 (7): 2836-2844


Diffusive Models of Membrane Permeation with Explicit Orientational Freedom
Jeffrey Comer; Klaus Schulten; Christophe Chipot;
Journal of Chemical Theory and Computation (2014) 10 (7): 2710-2718


Unveiling the Underlying Mechanism for Compression and Decompression Strokes of a Molecular Engine
Peng Liu; Christophe Chipot; Wensheng Cai; Xueguang Shao;
The Journal of Physical Chemistry C (2014) 118 (23): 12562-12567


Threading or Tumbling? Insight into the Self-Inclusion Mechanism of an
Ying Liu; Christophe Chipot; Xueguang Shao; Wensheng Cai;
The Journal of Physical Chemistry C (2014) 118 (33): 19380-19386


Evidence of Conducting Hydrophobic Nanopores Across Membranes in Response to an Electric Field
Francois Dehez; Lucie Delemotte; Peter Kramar; Damijan Miklavcic; Mounir Tarek;
The Journal of Physical Chemistry C (2014) 118 (13): 6752-6757


From Material Science to Avant-Garde Cuisine. The Art of Shaping Liquids into Spheres
Haohao Fu; Yingzhe Liu; Ferran Adria; Xueguang Shao; Wensheng Cai; Christophe Chipot;
The Journal of Physical Chemistry B (2014) 118 (40): 11747-11756


Cooperative Recruitment of Amphotericin B Mediated by a Cyclodextrin Dimer
Jia He; Christophe Chipot; Xueguang Shao; Wensheng Cai;
The Journal of Physical Chemistry C (2014) 118 (41): 24173-24180


Complexation mechanism of cucurbit[6]uril with hexamethylene diammonium cations in saline solution
Peng Liu; Xueguang Shao; Christophe Chipot; Wensheng Cai;
Phys. Chem. Chem. Phys. (2014) 14 (44): 33-24172


Multiple-Replica Strategies for Free-Energy Calculations in NAMD: Multiple-Walker Adaptive Biasing Force and Walker Selection Rules
Jeffrey Comer; James C. Phillips; Klaus Schulten; Christophe Chipot;
Journal of Chemical Theory and Computation (2014) 10 (12): 5276-5285


2013

The substrate specificity of the human ADP/ATP carrier AAC1
John Mifsud; Stephanie Ravaud; Eva-Maria Krammer; Chris Chipot; Edmund R. S. Kunji; Eva Pebay-Peyroula; Francois Dehez;
Molecular Membrane Biology (2013) 97 (2): 1990-168


Standard Binding Free Energies from Computer Simulations: What Is the Best Strategy?
James C. Gumbart; Benoit Roux; Christophe Chipot;
Journal of Chemical Theory and Computation (2013) 9 (1): 794-802


Efficient Determination of Protein–Protein Standard Binding Free Energies from First Principles
James C. Gumbart; Benoit Roux; Christophe Chipot;
Journal of Chemical Theory and Computation (2013) 9 (8): 3789-3798


Cyclodextrin-Mediated Recruitment and Delivery of Amphotericin B
Jia He; Christophe Chipot; Xueguang Shao; Wensheng Cai;
The Journal of Physical Chemistry C (2013) 117 (22): 11750-11756


Frontiers in High-Performance, Large-Scale Molecular Dynamics. 35 Years of Molecular-Dynamics Simulations of Biological Systems
Wensheng Cai; Chipot Christophe;
Acta Chimica Sinica (2013) 71 (2): 159-11756


Frontiers in free-energy calculations of biological systems
Christophe Chipot;
Wiley Interdisciplinary Reviews: Computational Molecular Science (2013) 9 (1): 876-89


On the Electroporation Thresholds of Lipid Bilayers: Molecular Dynamics Simulation Investigations
Andraz Polak; Daniel Bonhenry; Francois Dehez; Peter Kramar; Damijan Miklavcic; Mounir Tarek;
The Journal of Membrane Biology (2013) 112 (4): 13588-850


An ‘open’ structure of the RecOR complex supports ssDNA binding within the core of the complex
Jens Radzimanowski; Francois Dehez; Adam Round; Axel Bidon-Chanal; Sean McSweeney; Joanna Timmins;
Nucleic Acids Research (2013) 41 (16): 7972-7986


Calculating Position-Dependent Diffusivity in Biased Molecular Dynamics Simulations
Jeffrey Comer; Christophe Chipot; Fernando D. Gonzalez-Nilo;
Journal of Chemical Theory and Computation (2013) 9 (2): 876-882


Dangerous Liaisons between Detergents and Membrane Proteins. The Case of Mitochondrial Uncoupling Protein 2
Manuela Zoonens; Jeffrey Comer; Sandrine Masscheleyn; Eva Pebay-Peyroula; Christophe Chipot; Bruno Miroux; Francois Dehez;
Journal of the American Chemical Society (2013) 135 (40): 15174-15182


How Do Membrane Transporters Sense pH? The Case of the Mitochondrial ADP–ATP Carrier
Axel Bidon-Chanal; Eva-Maria Krammer; Delphine Blot; Eva Pebay-Peyroula; Christophe Chipot; Stephanie Ravaud; Francois Dehez;
The Journal of Physical Chemistry Letters (2013) 4 (21): 3787-3791


Water Conduction through a Peptide Nanotube
Jeffrey Comer; Francois Dehez; Wensheng Cai; Christophe Chipot;
The Journal of Physical Chemistry C (2013) 117 (50): 26797-26803


Effects of Phospholipid Composition on the Transfer of a Small Cationic Peptide Across a Model Biological Membrane
Daniel Bonhenry; Mounir Tarek; Francois Dehez;
Journal of Chemical Theory and Computation (2013) 9 (12): 5675-5684


2012

Water: The Forgotten Chemical, Edited by Denis Le Bihan and Hidenao Fukuyama. PanStanford Publishing, Singapore (2011), 399 pages.
Rudi Podgornik;
Journal of Biological Physics (2012) 38 (1): 9-12


Molecular Basis of Drug Resistance in A/H1N1 Virus
Ariela Vergara-Jaque; Horacio Poblete; Eric H. Lee; Klaus Schulten; Fernando Gonzalez-Nilo; Christophe Chipot;
Journal of Chemical Information and Modeling (2012) 52 (10): 2650-2656


The p7 Protein of Hepatitis C Virus Forms Structurally Plastic, Minimalist Ion Channels
Danielle E. Chandler; Francois Penin; Klaus Schulten; Christophe Chipot; Marco Punta;
PLoS Computational Biology (2012) 8 (9): e1002702-2656


A Toolkit for the Analysis of Free-Energy Perturbation Calculations
Peng Liu; Francois Dehez; Wensheng Cai; Christophe Chipot;
Journal of Chemical Theory and Computation (2012) 8 (8): 2606-2616


Impaired Transport of Nucleotides in a Mitochondrial Carrier Explains Severe Human Genetic Diseases
Stephanie Ravaud; Axel Bidon-Chanal; Iulia Blesneac; Paul Machillot; Celine Juillan-Binard; Francois Dehez; Chris Chipot; Eva Pebay-Peyroula;
ACS Chemical Biology (2012) 7 (7): 1164-1169


Insight into the Properties of Cardiolipin Containing Bilayers from Molecular Dynamics Simulations, Using a Hybrid All-Atom/United-Atom Force Field
Daniel Aguayo; Fernando D. Gonzalez-Nilo; Christophe Chipot;
Journal of Chemical Theory and Computation (2012) 8 (5): 1765-1773


Edge effects control helical wrapping of carbon nanotubes by polysaccharides
Yingzhe Liu; Christophe Chipot; Xueguang Shao; Wensheng Cai;
Nanoscale (2012) 343 (8): 2463-1773


Solvent-Controlled Shuttling in a Molecular Switch
Peng Liu; Christophe Chipot; Xueguang Shao; Wensheng Cai;
The Journal of Physical Chemistry C (2012) 116 (7): 4471-4476


Conformational Free-Energy Landscapes for a Peptide in Saline Environments
Timothy  J. Gaborek; Christophe Chipot; Jeffry  D. Madura;
Biophysical Journal (2012) 103 (12): 2513-2520


How Do α-Cyclodextrins Self-Organize on a Polymer Chain?
Peng Liu; Christophe Chipot; Xueguang Shao; Wensheng Cai;
The Journal of Physical Chemistry C (2012) 116 (33): 17913-17918


2011

Free Energy of Nascent-Chain Folding in the Translocon
James Gumbart; Christophe Chipot; Klaus Schulten;
Journal of the American Chemical Society (2011) 133 (19): 7602-7607


Cytoplasmic Domain Filter Function in the Mechanosensitive Channel of Small Conductance
Ramya Gamini; Marcos Sotomayor; Christophe Chipot; Klaus Schulten;
Biophysical Journal (2011) 101 (1): 80-89


Enhanced Sampling of Multidimensional Free-Energy Landscapes Using Adaptive Biasing Forces
Christophe Chipot; Tony Lelievre;
SIAM Journal on Applied Mathematics (2011) 71 (5): 1673-1695


Reconciling alternate methods for the determination of charge distributions: a probabilistic approach to high-dimensional least-squares approximations
Nicolas Champagnat; Chris Chipot; Erwan Faou;
Journal of Mathematical Chemistry (2011) 24 (3): 997-324


Structural Characterization of Micelles Formed of Cholesteryl-Functionalized Cyclodextrins
Teng Wang; Christophe Chipot; Xueguang Shao; Wensheng Cai;
Langmuir (2011) 27 (1): 91-97


Gating of a pH-Sensitive K2P Potassium Channel by an Electrostatic Effect of Basic Sensor Residues on the Selectivity Filter
Leandro Zuniga; Valeria Marquez; Fernando D. Gonzalez-Nilo; Christophe Chipot; L. Pablo Cid; Francisco V. Sepulveda; Maria Isabel Niemeyer; Bradley Launikonis;
PLoS ONE (2011) 14 (1): 354-97


Free-Energy Landscape of the Helical Wrapping of a Carbon Nanotube by a Polysaccharide
Yingzhe Liu; Christophe Chipot; Xueguang Shao; Wensheng Cai;
The Journal of Physical Chemistry C (2011) 115 (5): 1851-1856


Polarization effects in molecular interactions
F. Javier Luque; Francois Dehez; Christophe Chipot; Modesto Orozco;
Wiley Interdisciplinary Reviews: Computational Molecular Science (2011) 25 (5): 1504-854


Free-energy cost for translocon-assisted insertion of membrane proteins
J. Gumbart; C. Chipot; K. Schulten;
Proceedings of the National Academy of Sciences (2011) 26 (16): 1781-3601


Oligomerization State of Photosynthetic Core Complexes Is Correlated with the Dimerization Affinity of a Transmembrane Helix
Jen Hsin; Loren M. LaPointe; Alla Kazy; Christophe Chipot; Alessandro Senes; Klaus Schulten;
Journal of the American Chemical Society (2011) 133 (35): 14071-14081


The effects of 7-dehydrocholesterol on the structural properties of membranes
Yingzhe Liu; Christophe Chipot; Xueguang Shao; Wensheng Cai;
Physical Biology (2011) 8 (5): 056005-14081


Free Energy Calculations for Cyclodextrin Inclusion Complexes
Wen Sheng Cai; Teng Wang; Ying Zhe Liu; Peng Liu; Christophe Chipot; Xue Guang Shao;
Current Organic Chemistry (2011) 15 (6): 839-847


Recognition of methylated DNA through methyl-CpG binding domain proteins
Xueqing Zou; Wen Ma; Ilia A. Solov'yov; Christophe Chipot; Klaus Schulten;
Nucleic Acids Research (2011) 40 (6): 2747-2758


2010

Exploring Multidimensional Free Energy Landscapes Using Time-Dependent Biases on Collective Variables
Jerome Henin; Giacomo Fiorin; Christophe Chipot; Michael L. Klein;
Journal of Chemical Theory and Computation (2010) 6 (1): 35-47


On the Antibacterial Action of Cyclic Peptides: Insights from Coarse-Grained MD Simulations
Adil Khalfa; Mounir Tarek;
The Journal of Physical Chemistry B (2010) 114 (8): 2676-2684


Affinity of C
Sebastian Kraszewski; Mounir Tarek; Werner Treptow; Christophe Ramseyer;
ACS Nano (2010) 4 (7): 4158-4164


Effect of Sensor Domain Mutations on the Properties of Voltage-Gated Ion Channels: Molecular Dynamics Studies of the Potassium Channel Kv1.2
Lucie Delemotte; Werner Treptow; Michael L. Klein; Mounir Tarek;
Biophysical Journal (2010) 99 (9): L72-L74


Potential of Mean Force Calculations: A Multiple-Walker Adaptive Biasing Force Approach
K. Minoukadeh; C. Chipot; T. Lelievre;
Journal of Chemical Theory and Computation (2010) 6 (4): 1008-1017


Solubilizing Carbon Nanotubes through Noncovalent Functionalization. Insight from the Reversible Wrapping of Alginic Acid around a Single-Walled Carbon Nanotube
Yingzhe Liu; Christophe Chipot; Xueguang Shao; Wensheng Cai;
The Journal of Physical Chemistry B (2010) 114 (17): 5783-5789


Thermodynamic Insights into the Dynamic Switching of a Cyclodextrin in a Bistable Molecular Shuttle
Peng Liu; Wensheng Cai; Christophe Chipot; Xueguang Shao;
The Journal of Physical Chemistry Letters (2010) 1 (12): 1776-1780


Good Practices in Free-Energy Calculations
Andrew Pohorille; Christopher Jarzynski; Christophe Chipot;
The Journal of Physical Chemistry B (2010) 114 (32): 10235-10253


Solubilities Inferred from the Combination of Experiment and Simulation. Case Study of Quercetin in a Variety of Solvents
Latifa Chebil; Christophe Chipot; Fabien Archambault; Catherine Humeau; Jean Marc Engasser; Mohamed Ghoul; Francois Dehez;
The Journal of Physical Chemistry B (2010) 114 (38): 12308-12313


NMR Structure and Ion Channel Activity of the p7 Protein from Hepatitis C Virus
Roland Montserret; Nathalie Saint; Christophe Vanbelle; Andres Gerardo Salvay; Jean-Pierre Simorre; Christine Ebel; Nicolas Sapay; Jean-Guillaume Renisio; Anja Bockmann; Eike Steinmann; Thomas Pietschmann; Jean Dubuisson; Christophe Chipot; Francois Penin;
Journal of Biological Chemistry (2010) 1330 (41): 284-31461


2009

Molecular dynamics simulation studies of coupled protein and water dynamics. In On the Computational Study of Energy Flow in Proteins
Tobias, D.J.; Sengupta, N. and Tarek, M.
2009


Inclusion Mechanism of Steroid Drugs into β-Cyclodextrins. Insights from Free Energy Calculations
Wensheng Cai; Tingting Sun; Peng Liu; Christophe Chipot; Xueguang Shao;
The Journal of Physical Chemistry B (2009) 113 (22): 7836-7843


Self assembly of peptides near or within membranes using coarse grained MD simulations
A. Khalfa; W. Treptow; B. Maigret; M. Tarek;
Chemical Physics (2009) 358 (1-2): 161-170


Hydration dynamics of purple membranes
Douglas J. Tobias; Neelanjana Sengupta; Mounir Tarek;
Faraday Discuss. (2009) 76 (1-2): 928-116


Initial Response of the Potassium Channel Voltage Sensor to a Transmembrane Potential
Werner Treptow; Mounir Tarek; Michael L. Klein;
Journal of the American Chemical Society (2009) 131 (6): 2107-2109


A Glycophorin A-Like Framework for the Dimerization of Photosynthetic Core Complexes
Jen Hsin; Christophe Chipot; Klaus Schulten;
Journal of the American Chemical Society (2009) 131 (47): 17096-17098


Membrane Curvature Induced by Aggregates of LH2s and Monomeric LH1s
Danielle E. Chandler; James Gumbart; John D. Stack; Christophe Chipot; Klaus Schulten;
Biophysical Journal (2009) 97 (11): 2978-2984


High-Chloride Concentrations Abolish the Binding of Adenine Nucleotides in the Mitochondrial ADP/ATP Carrier Family
Eva-Maria Krammer; Stephanie Ravaud; Francois Dehez; Annie Frelet-Barrand; Eva Pebay-Peyroula; Christophe Chipot;
Biophysical Journal (2009) 97 (10): L25-L27


Polarizable Intermolecular Potentials for Water and Benzene Interacting with Halide and Metal Ions
Fabien Archambault; Christophe Chipot; Ignacio Soteras;$F. Jcvyer Luque; Klaus Schulten; Francois Dehez;
Journal of Chemical Theory and Computation (2009) 5 (11): 3022-3031


Methods in Molecular BiologyHepatitis C: Methods and ProtocolsStructural and Functional Analysis of the HCV p7 Protein
Hengli Tang; Nathalie Saint; Roland Montserret; Christophe Chipot; Francois Penin;
Journal of Chemical Theory and Computation (2009) 510 (11): 125-143


A molecular modelling study to rationalize the regioselectivity in acylation of flavonoid glycosides catalyzed by Candida antarctica lipase B
Eduardo B. De Oliveira; Catherine Humeau; Latifa Chebil; Elaine R. Maia; Francois Dehez; Bernard Maigret; Mohamed Ghoul; Jean-Marc Engasser;
Journal of Molecular Catalysis B: Enzymatic (2009) 59 (1-3): 96-105


2008

Schulten, K. - Understanding the structure and the function of membrane proteins using free energy calculations. in Biophysical approaches of structure and functions of membrane proteins
Pebay-Peyroula, E.; Chipot, C.; Schulten, K.
2008


Diffusion of Glycerol through Escherichia coli Aquaglyceroporin GlpF
Jerome Henin; Emad Tajkhorshid; Klaus Schulten; Christophe Chipot;
Biophysical Journal (2008) 94 (3): 832-839


Gating Motions in Voltage-Gated Potassium Channels Revealed by Coarse-Grained Molecular Dynamics Simulations
Werner Treptow; Siewert-J Marrink; Mounir Tarek;
The Journal of Physical Chemistry B (2008) 112 (11): 3277-3282


Spatial Arrangement of α-Cyclodextrins in a Rotaxane. Insights from Free-Energy Calculations
Yanmin Yu; Wensheng Cai; Christophe Chipot; Tingting Sun; Xueguang Shao;
The Journal of Physical Chemistry B (2008) 112 (17): 5268-5271


Can the anomalous aqueous solubility of β-cyclodextrin be explained by its hydration free energy alone?
Wensheng Cai; Tingting Sun; Xueguang Shao; Christophe Chipot;
Physical Chemistry Chemical Physics (2008) 115 (22): 6866-5271


The role of protein–solvent hydrogen bond dynamics in the structural relaxation of a protein in glycerol versus water
Mounir Tarek; Douglas J. Tobias;
European Biophysics Journal (2008) 71 (17): 91-709


Binding of ADP in the Mitochondrial ADP/ATP Carrier Is Driven by an Electrostatic Funnel
Francois Dehez; Eva Pebay-Peyroula; Christophe Chipot;
Journal of the American Chemical Society (2008) 130 (38): 12725-12733


Milestones in the Activation of a G Protein-Coupled Receptor. Insights from Molecular-Dynamics Simulations into the Human Cholecystokinin Receptor-1
Christophe Chipot;
Journal of Chemical Theory and Computation (2008) 4 (12): 2150-2159


Modeling Membranes under a Transmembrane Potential
Lucie Delemotte; Francois Dehez; Werner Treptow; Mounir Tarek;
The Journal of Physical Chemistry B (2008) 112 (18): 5547-5550


Fingerprints of Amorphous Icelike Behavior in the Vibrational Density of States of Protein Hydration Water
A. Paciaroni; A. Orecchini; E. Cornicchi; M. Marconi; C. Petrillo; M. Haertlein; M. Moulin; H. Schober; M. Tarek; F. Sacchetti;
Physical Review Letters (2008) 21 (14): 129-2109


An ab initio strategy for handling induction phenomena in metal ion complexes
Francois Dehez; Fabien Archambault; Ignacio Soteras Gutierrez; F. Javier Luque; Christophe Chipot;
Molecular Physics (2008) 106 (12): 1685-1696


Methods in Molecular BiologyMolecular Modeling of ProteinsFree Energy Calculations Applied to Membrane Proteins
John M. Walker; Andreas Kukol; Christophe Chipot;
Wiley Interdisciplinary Reviews: Computational Molecular Science (2008) 443 (5): 121-144


2007

Functional dissociation between apelin receptor signaling and endocytosis: implications for the effects of apelin on arterial blood pressure
Iturrioz, X.; El Messari, S.; De Mota, N.; Fassot, C.; Alvear-Perez, R.; Maigret, B.; Llorens-Cortes, C.
Archives Des Maladies Du Coeur Et Des Vaisseaux (2007) 100 704-708


Functional dissociation between apelin receptor signaling and enclocytosis: implications for the effects of apelin on arterial blood pressure
Iturrioz, X.; El Messari, S.; De Mota, N.; Fassot, C.; Alvear-Perez, R.; Maigret, B.; Llorens-Cortes, C.
Nourncl0Of Hypertension (2007) 25 (12): A1


Free energy calculations. Theory and applications in chemistry and biology
Chipot, C.; Pohorille, A.
2007


Solubility of Flavonoids in Organic Solvents
Latifa Chebil; Catherine Humeau; Julie Anthoni; Francois Dehez; Jean-Marc Engasser; Mohamed Ghoul;
Engineering Data (2007) 52 (5): 1552-1556


Energetics of Ion Transport in a Peptide Nanotube
Francois Dehez; Mounir Tarek; Christophe Chipot;
The Journal of Physical Chemistry B (2007) 111 (36): 10633-10635


Discovering new inhibitors of bacterial glucosamine-6P synthase (GlmS) by docking simulations
Nicolas Floquet; Celine Richez; Philippe Durand; Bernard Maigret; Bernard Badet; Marie-Ange Badet-Denisot;
Medicinal Chemistry Letters (2007) 17 (7): 1966-1970


Role of water molecules for binding inhibitors in the SH2 domain of Grb2: A molecular dynamics study
Vincent Leroux; Nohad Gresh; Wang-Qing Liu; Christiane Garbay; Bernard Maigret;
Journal of Molecular Structure: THEOCHEM (2007) 806 (1-3): 51-66


Large-scale molecular dynamics of a G protein-coupled receptor, the human 5-HT4 serotonin receptor, in a lipid bilayer
L. Rivail; C. Chipot; B. Maigret; I. Bestel; S. Sicsic; M. Tarek;
Journal of Molecular Structure: THEOCHEM (2007) 817 (1-3): 19-26


Modeling Induction Phenomena in Intermolecular Interactions with an Ab Initio Force Field
Francois Dehez; Janos G. Angyan; Ignacio Soteras Gutierrez; F. Javier Luque; Klaus Schulten; Christophe Chipot;
Journal of Chemical Theory and Computation (2007) 3 (6): 1914-1926


Derivation of Distributed Models of Atomic Polarizability for Molecular Simulations
Ignacio Soteras; Carles Curutchet; Axel Bidon-Chanal; Francois Dehez; Janos G. Angyan; Modesto Orozco; Christophe Chipot; F. Javier Luque;
Journal of Chemical Theory and Computation (2007) 3 (6): 1901-1913


2006

Interaction of a peptide nanotube with a water–membrane interface
Christophe Chipot; Mounir Tarek;
Physical Biology (2006) 3 (1): S20-S25


Hydrogen-bonding patterns of cholesterol in lipid membranes
Jerome Henin; Christophe Chipot;
Chemical Physics Letters (2006) 425 (4-6): 329-335


Probing a Model of a GPCR/Ligand Complex in an Explicit Membrane Environment: The Human Cholecystokinin-1 Receptor
Jerome Henin; Bernard Maigret; Mounir Tarek; Chantal Escrieut; Daniel Fourmy; Christophe Chipot;
Biophysical Journal (2006) 90 (4): 1232-1240


Conformational Equilibrium in Alanine-Rich Peptides Probed by Reversible Stretching Simulations
Jerome Henin; Klaus Schulten; Christophe Chipot;
The Journal of Physical Chemistry B (2006) 110 (33): 16718-16723


NMR Structure and Molecular Dynamics of the In-Plane Membrane Anchor of Nonstructural Protein 5A from Bovine Viral Diarrhea Virus
Nicolas Sapay; Roland Montserret; Christophe Chipot; Volker Brass; Darius Moradpour; Gilbert Deleage; Francois Penin;
Biochemistry (2006) 45 (7): 2221-2233


Environment of the Gating Charges in the Kv1.2 Shaker Potassium Channel
Werner Treptow; Mounir Tarek;
Biophysical Journal (2006) 90 (9): L64-L66


Molecular Dynamics Study of the Inclusion of Cholesterol into Cyclodextrins
Yanmin Yu; Christophe Chipot; Wensheng Cai; Xueguang Shao;
The Journal of Physical Chemistry B (2006) 110 (12): 6372-6378


Hydrogen-bonding patterns of cholesterol in lipid membranes
Jerome Henin; Christophe Chipot;
Chemical Physics Letters (2006) 425 (4-6): 329-335


PGY Repeats and N-Glycans Govern the Trafficking of Paranodin and Its Selective Association with Contactin and Neurofascin-155
C. Bonnon; C. Bel; L. Goutebroze; B. Maigret; J.-A. Girault; C. Faivre-Sarrailh;
Molecular Biology of the Cell (2006) 18 (1): 229-241


K+ Conduction in the Selectivity Filter of Potassium Channels Is Monitored by the Charge Distribution along Their Sequence
Werner Treptow; Mounir Tarek;
Biophysical Journal (2006) 91 (10): L81-L83


Molecular Restraints in the Permeation Pathway of Ion Channels
Werner Treptow; Mounir Tarek;
Biophysical Journal (2006) 91 (3): L26-L28


2005

Activation of Shaker B, a voltage-gated potassium channel
Tarek, M.; Treptow, W.
Abstracts Of Papers Of The American Chemical Society (2005) 229 057-COMP


Can free energy calculations be fast and accurate at the same time? Binding of low-affinity, non-peptide inhibitors to the SH2 domain of the src protein
Christophe Chipot; Xavier Rozanska; Surjit B. Dixit;
Journal of Computer-Aided Molecular Design (2005) 66 (11): 123-770


Exploring the free-energy landscape of a short peptide using an average force
Christophe Chipot; Jerome Henin;
The Journal of Chemical Physics (2005) 123 (24): 244906-770


Long-range electrostatic interactions in hybrid quantum and molecular mechanical dynamics using a lattice summation approach
Francois Dehez; Marilia T. C. Martins-Costa; Daniel Rinaldi; Claude Millot;
The Journal of Chemical Physics (2005) 7 (23): 82-770


Insights into the Recognition and Association of Transmembrane α-Helices. The Free Energy of α-Helix Dimerization in Glycophorin A
Jerome Henin; Andrew Pohorille; Christophe Chipot;
Journal of the American Chemical Society (2005) 127 (23): 8478-8484


Scalable molecular dynamics with NAMD
James C. Phillips; Rosemary Braun; Wei Wang; James Gumbart; Emad Tajkhorshid; Elizabeth Villa; Christophe Chipot; Robert D. Skeel; Laxmikant Kale; Klaus Schulten;
Journal of Computational Chemistry (2005) 84 (16): 242-1802


Membrane Electroporation: A Molecular Dynamics Simulation
Mounir Tarek;
Biophysical Journal (2005) 88 (6): 4045-4053


Favorable Entropy of Aromatic Clusters in Thermophilic Proteins
Bruno Trebbi; Francois Dehez; Patrick W. Fowler; Francesco Zerbetto;
The Journal of Physical Chemistry B (2005) 109 (38): 18184-18188


2004

Methyl Group Dynamics as a Probe of the Protein Dynamical Transition
Joseph E. Curtis; Mounir Tarek; Douglas J. Tobias;
Journal of the American Chemical Society (2004) 126 (49): 15928-15929


Overcoming free energy barriers using unconstrained molecular dynamics simulations
Jerome Henin; Christophe Chipot;
The Journal of Chemical Physics (2004) 17 (7): 1112-2914


Coupled Motions between Pore and Voltage-Sensor Domains: A Model for Shaker B, a Voltage-Gated Potassium Channel
Werner Treptow; Bernard Maigret; Christophe Chipot; Mounir Tarek;
Biophysical Journal (2004) 87 (4): 2365-2379


2003

Membrane peptides and their role in protobiological evolution
Pohorille, A.; Wilson, M.A.; Chipot, C.
Origins Of Life And Evolution Of Biospheres (2003) 33 (2): 173-197


Rational determination of charge distributions for free energy calculations
Christophe Chipot;
Journal of Computational Chemistry (2003) 10 (4): 1-415


Non-Arrhenius Behavior in the Unfolding of a Short, Hydrophobic α-Helix. Complementarity of Molecular Dynamics and Lattice Model Simulations
Olivier Collet; Christophe Chipot;
Journal of the American Chemical Society (2003) 125 (21): 6573-6580


Influence of Anesthetic and Nonimmobilizer Molecules on the Physical Properties of a Polyunsaturated Lipid Bilayer
Laure Koubi; Leonor Saiz; Mounir Tarek; Daphna Scharf; Michael L. Klein;
The Journal of Physical Chemistry B (2003) 107 (51): 14500-14508


Characterization of sub-nanosecond dynamics of the molten globule state of α-lactalbumin using quasielastic neutron scattering and molecular dynamics simulations
Mounir Tarek; Dan A. Neumann; Douglas J. Tobias;
Chemical Physics (2003) 292 (2-3): 435-443


Molecular Dynamics Investigation of an Oriented Cyclic Peptide Nanotube in DMPC Bilayers
Mounir Tarek; Bernard Maigret; Christophe Chipot;
Biophysical Journal (2003) 85 (4): 2287-2298


2002

Rational Determination of Transfer Free Energies of Small Drugs across the Water−Oil Interface
Delphine Bas; Delphine Dorison-Duval; Stephanie Moreau; Pierre Bruneau; Christophe Chipot;
Journal of Medicinal Chemistry (2002) 45 (1): 151-159


Free Energy Calculations. The Long and Winding Gilded Road
Christophe Chipot; David A. Pearlman;
Molecular Simulation (2002) 28 (1-2): 1-12


Single-Particle and Collective Dynamics of Protein Hydration Water: A Molecular Dynamics Study
M. Tarek; D. J. Tobias;
Physical Review Letters (2002) 17 (27): 370-12


2001

Insights into the Self-Assembly of Small, Organic Molecules:  Case Study of 2,4,6-Trichlorophenol
Christophe Chipot;
The Journal of Physical Chemistry B (2001) 105 (25): 5987-5993


Can Absolute Free Energies of Association Be Estimated from Molecular Mechanical Simulations? The Biotin−Streptavidin System Revisited
Surjit B. Dixit; Christophe Chipot;
The Journal of Physical Chemistry A (2001) 105 (42): 9795-9799


2000

Structural analysis of the KGD sequence loop of barbourin, an alpha(IIb)beta(3)-specific disintegrin
Minoux, H.; Chipot, C.; Brown, D.; Maigret, B.
Journal Of Computer-Aided Molecular Design (2000) 14 (4): 317-327


Parallel molecular dynamics using OpenMP on a shared memory machine
Raphael Couturier; Christophe Chipot;
Computer Physics Communications (2000) 124 (1): 49-59


Fast evaluation of induction energies: a second-order perturbation theory approach
Christophe Chipot; F.Javier Luque;
Chemical Physics Letters (2000) 332 (1-2): 190-198


Modeling ion–ion interaction in proteins: A molecular dynamics free energy calculation of the guanidinium-acetate association
Xavier Rozanska; Christophe Chipot;
The Journal of Chemical Physics (2000) 112 (22): 9691-9694


Recent publications



Haohao Fu; Xueguang Shao; Christophe Chipot; Wensheng Cai;
Chem. Sci. (2017) 139 (7): 293-5094

The Extended Generalized Adaptive Biasing Force Algorithm for Multidimensional Free-Energy Calculations
Tanfeng Zhao; Haohao Fu; Tony Lelievre; Xueguang Shao; Christophe Chipot; Wensheng Cai;
Journal of Chemical Theory and Computation (2017) 13 (4): 1566-1576

Tribute to Klaus Schulten
Emad Tajkhorwhid;"Cxristophe Chipot;
The Journal of Physical Chemistry B (2017) 121 (15): 3203-3205

News

- Renewal of the Laboratoire International Associé CNRS-University of Illinois at Urbana-Champaign on November 2016
- An update of ParseFEP is available in the latest version of VMD.
- 新的分子动力学讲义 (Dissemination).
 

Contact

Laboratoire International Associé
CNRS-UIUC
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Université de Lorraine, B.P. 70239
54506 Vandoeuvre-lès-Nancy Cedex, France
 
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