2016

Liu, P.; Shao, X.; Chipot, C.; Cai, W.,
The true nature of rotary movements in rotaxanes
Chem. Sci.
  2016,  (7), 457-462.
dx.doi.org

Miyagi, A.; Chipot, C.; Rangl, M.; Scheuring, S.
High-speed atomic force microscopy shows that annexin V stabilizes membranes on the second timescale
Nature Nanotechnology
  2016,  (11),  783-790 .
dx.doi.org

Vukovic, L.; Chipot, C.; Makino, D.; Conti, E.; Schulten, K
Molecular mechanism of processive 3' to 5' RNA translocation in the active subunit of the RNA exosome complex
J. Am. Chem. Soc.
  2016,  (139), 4069-4078.
dx.doi.org

Gumbart, J. C.; Chipot, C
Decrypting protein insertion through the translocon with free–energy calculations
Biochim. Biophys. Acta Biomembr.
  2016,  (1858), 1663-1671.
dx.doi.org

Liu, Y.; Chipot, C.; Shao, X.; Cai, W.
How does the solvent modulate shuttling in a pillararene/imidazolium [2]rotaxane? Insights from free–energy calculations
J. Phys. Chem. C
  2016,  (120), 6287-6293.
dx.doi.org

Fu, H.; Shao, X.; Chipot, C.; Cai, W.
Extended adaptive biasing force algorithm. An on–the–fly implementation for accurate free–energy calculations
J. Chem. Theory Comput.
  2016,  (12), 3506-3513.
dx.doi.org

Lee, C. T.; Comer, J.; Herndon, C.; Leung, N.; Pavlova, A.; Swift, R. V.; Tung, C.; Rowley, C. N.; Amaro, R. E.; Chipot, C.; Wang, Y.; Gumbart, J. C.
Simulation-Based Approaches for Determining Membrane Permeability of Small Compounds.
J. Chem. Inf. Model.
  2016,  (56), 721-733.
dx.doi.org

Ramadoss, V.; Dehez, F.; Chipot, C
AlaScan: A graphical user interface for alanine scanning free–energy calculations.
J. Chem. Info. Model.
  2016,  (56), 1122-1126.
dx.doi.org

Bozzi, A. T.; Bane, L. B.; Weihofen, W. A.; McCabe, A. L.; Singharoy, A.; Chipot, C. J.; Schulten, K.; Gaudet, R.
Conserved methionine dictates substrate preference in Nramp–family divalent metal transporters
Proc. Natl. Acad. Sci. U.S.A.
  2016,  (113), 10310-10315.
dx.doi.org

Jo, S.; Suh, D.; He, Z.; Chipot, C.; Roux, B.
Leveraging the information from Markov state models to improve the convergence of umbrella sampling simulations
J. Phys. Chem. B
  2016,  (120), 8733-8742.
dx.doi.org

Holzmann, Nicole; Chipot, Christophe; Penin, François; Dehez, François
Assessing the physiological relevance of alternate architectures of the p7 protein of hepatitis C virus in different environments
Bioorg. Med. Chem
  2016,  (24), 4920-4927.
dx.doi.org

Gattuso, H.; Durand, E.; Bignon, E.; Morell, C.; Georgakilas, A. G.; Dumont, E.; Chipot, C.; Dehez, F.; Monari, A.
Repair rate of clustered abasic DNA lesions by human endonuclease: Molecular bases of sequence specificity
J. Phys. Chem. Lett
  2016,  (19), 3760-3765.
dx.doi.org

Wang, S.; Zhao, T.; Shao, X.; Chipot, C.; Cai, W.
Complex movements in rotaxanes: Shuttling coupled with conformational transition of cyclodextrins
J. Phys. Chem. C
  2016,  (120), 19479-19486.
dx.doi.org

Bignon, E.; Gattuso, H.; Morell, C.; Dehez, F.; Georgakilas, A. G.; Monari, A. & Dumont, E.
Correlation of bistranded clustered abasic DNA lesion processing with structural and dynamic DNA helix distortion.
Nucleic Acids Res.
  2016,  (44), 8588-8599.
dx.doi.org

2015

Fu, H.; Comer, J.; Cai, W.; Chipot, C
Sonoporation at small and large length scales. Effect of cavitation bubble collapse on membranes
J. Phys. Chem. Letters
  2015, 6 (3), 413-418.
dx.doi.org

Comer, J.; Gumbart, J. C.; Hénin, J.; Lelièvre, T.; Pohorille, A.; Chipot, C.
The adaptive biasing force method: Everything you always wanted to know, but were afraid to ask
J. Phys. Chem. B
  2015, 119 (3), 1129-1151.
dx.doi.org

Jo, S.; Chipot, C.; Roux, B.
Efficient determination of relative entropy using combined temperature and Hamiltonian replica-exchange molecular dynamics
J. Chem. Theory Comput.
  2015, 11 (5), 2234-2244.
dx.doi.org

Liu, Y.; Chipot, C.; Shao, X.; Cai, W.
What causes tumbling of altro-a-CD derivatives? Insight from computer simulations
RSC Advances
  2015,  (5), 57309-57317.
dx.doi.org

Fu, H.; Chipot, C.; Shao, X.; Cai,W.
Why do the structural properties of complexes formed by glucans and carbon nanotubes differ so much?
RSC Advances
  2015,  (5), 95682-95689.
dx.doi.org

Dehez, F. (Book Chapter)
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.
Oxford University Press
  2015,  (ISBN : 978-0-19-875295-0 ), .

2014

Chipot, C.;
Frontiers in Free-Energy Calculations of Biological Systems
WIREs Comput. Mol. Sci.
  2014, 4 (1), 71-89.
dx.doi.org

Comer, J.; Roux, B.; Chipot, C.;
Achieving ergodic sampling using replica-exchange free-energy calculations
Mol. Sim.
  2014, 40 (1-3),  218-228.
dx.doi.org

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

Comer, J.; Schulten, K.; Chipot, C.
Calculation of lipid-bilayer permeabilities using an average force
J.Chem. Theory Comput.
  2014, 10 (2), 554-564.
dx.doi.org

Hazel, A.; Chipot, C.; Gumbart, J. C.
Thermodynamics of deca-alanine folding in water
J. Chem. Theory Comput.
  2014, 10 (7), 2836-2844.
dx.doi.org

Comer, J. R.; Schulten, K.; Chipot, C.
Diffusive models of membrane permeation with explicit orientational freedom
J. Chem. Theory Comput.
  2014, 10 (7), 2710-2718.
dx.doi.org

Liu, P.; Chipot, C.; Cai, W.; Shao, X.
Unveiling the underlying mechanism for compression and decompression strokes of a molecular engine
J. Phys. Chem. C
  2014, 118 (23), 12562-12567.
dx.doi.org

Liu, Y.; Chipot, C.; Shao, X.; Cai, W.
Threading or tumbling? Insight into the self-inclusion mechanism of an altro-α-cyclodextrin derivative
J. Phys. Chem. C
  2014, 118 (33), 19380-19386.
dx.doi.org

Dehez, F.; Delemotte, L.; Kramar, P.; Miklavcic, D.; Tarek, M.
Evidence of conducting hydrophobic nanopores across membranes in response to an electric field
J. Phys. Chem. C
  2014, 118 (13), 6752-6757.
dx.doi.org

Fu, H.; Liu, Y.; Adrià, F.; Shao, X.; Cai, W.; Chipot, C.,
From material science to avant-garde cuisine. The art of shaping liquids into spheres
J. Phys. Chem. C
  2014, 118 (40), 11747-11756.
dx.doi.org

He, J.; Chipot, C.; Shao, X.; Cai,W
Cooperative recruitment of amphotericin B mediated by a cyclodextrin dimer
J. Phys. Chem. C
  2014, 118 (41), 24173-24180.
dx.doi.org

Liu, P.; Shao, X.; Chipot, C.; Cai, W.
Complexation mechanism of cucurbit[6]uril with hexamethylene diammonium cations in saline solution
Phys. Chem. Chem. Phys
  2014, - (16), 24169-24172.
dx.doi.org

Comer, J.; Phillips, J.; Schulten, K.; Chipot, C.
Multiple-walker strategies for free-energy calculations in NAMD: Shared adaptive biasing force and walker selection rules
J. Chem. Theor. Comput.
  2014, 10 (12), 5276-5285.
dx.doi.org

2013

Mifsud, J.; Ravaud, S.; Krammer, E.-M.; Chipot, C.; Kunji, E.R.S.; Pebay-Peyroula, E.; Dehez, F.
The substrate specificity of the human ADP/ATP carrier AAC1
Molecular Membrane Biology
  2013, 30 (2), 160-168.
dx.doi.org

Gumbart, J.C.; Roux, B.; Chipot, C.
Standard Binding Free Energies from Computer Simulations: What Is the Best Strategy?
J. Chem. Theory Comput.
  2013, 9 (1), 794-802.
dx.doi.org

Gumbart, J. C.; Roux, B.; Chipot, C.
Efficient determination of protein-protein standard binding free energies from first principles
J. Chem. Theor. Comput.
  2013, 9 (8), 3789-3798.
dx.doi.org

He, J.; Chipot, C.; Shao, X.; Cai, W.
Cyclodextrin-mediated recruitment and delivery of amphotericin B
J. Phys. Chem. C
  2013, 117 (22), 11750-11756.
dx.doi.org

Cai, W. and Chipot, C.
Frontiers in high-performance, large-scale molecular dynamics. 35 years of molecular-dynamics simulations of biological systems
Acta Chimica SinicaActa Chimica Sinica
  2013, 71 (2), 159-168.
dx.doi.org

Polak, A.; Bonhenry, D.; Dehez, F.; Kramar, P.; Miklavčič, D.; Tarek, M.;
On the Electroporation Thresholds of Lipid Bilayers: Molecular Dynamics Simulation Investigations
J. Membr. Biol.J. Membr. Biol.
  2013, 246 (50), 843-850.
dx.doi.org

Radzimanowski, J.; Dehez, F.; Round, A.; Bidon-Chanal, A.; McSweeney, S.; Timmins, J.;
An "open" structure of the RecOR complex supports ssDNA binding within the core of the complex
Nucl. Acids Res.
  2013, 41 (16 ), 7972-7986.
dx.doi.org

Comer, J.; Chipot, C.; Fernando, D.; Gonzalez-Nilo,
Calculating position-dependent di ffusivity in biased molecular dynamics simulations
J. Chem. Theor. Comput.
  2013, 9 (2), 876-882.
dx.doi.org

Zoonens, M.; Comer, J.; Masscheleyn, S.; Pebay-Peyroula, E.; Chipot, C.; Miroux, B. ; Dehez, F.;
Dangerous Liaisons between Detergents and Membrane Proteins. The Case of Mitochondrial Uncoupling Protein 2
J. Am. Chem. Soc.
  2013, 135 (40), 15174-15182.
dx.doi.org

Bidon-Chanal, A.; Krammer, E-M.; Blot, D.; Pebay-Peyroula, E.; Chipot, C.; Ravaud, S.; Dehez, F.;
How do membrane transporters sense pH ? The case of the mitochondrial ADP-ATP carrier
J. Phys. Chem. Lett.
  2013, 4 (21), 3787-3791.
dx.doi.org

Comer, J.; Dehez, F.; Cai, W.; Chipot, C.;
Water conduction through a peptide nanotube
J. Phys. Chem. C
  2013, 117 (50), 26797-26803.
dx.doi.org

Bonhenry, D.; Tarek, M.; Dehez, F.;
Effects of phospholipid composition on the transfer of a small cationic peptide across a model biological membrane
J. Chem. Theory Comput.
  2013, 9 (12), 5675-5684.
dx.doi.org

2012

Vergara-Jaque, A.; Poblete, H.; Lee, E.H.; Schulten, K.; González-Nilo, F.; Chipot, C.
Molecular Basis of Drug Resistance in A/H1N1 Virus
J. Chem. Inf. Model.
  2012, 52 (10), 2650-2656.
dx.doi.org

Chandler, D.E.; Penin, F.; Schulten, K.; Chipot, C.
The p7 Protein of Hepatitis C Virus Forms Structurally Plastic, Minimalist Ion Channels
PLoS Comput Biol
  2012, 8 (9), e1002702.
dx.doi.org

Liu, P.; Dehez, F.; Cai, W.; Chipot, C.
A Toolkit for the Analysis of Free-Energy Perturbation Calculations
J. Chem. Theory Comput.
  2012, 8 (8), 2606-2616.
dx.doi.org

Ravaud, S.; Bidon-Chanal, A.; Blesneac, I.; Machillot, P.; Juillan-Binard, C.; Dehez, F.; Chipot, C.; Pebay-Peyroula, E.
Impaired Transport of Nucleotides in a Mitochondrial Carrier Explains Severe Human Genetic Diseases
ACS Chem. Biol.
  2012, 7 (7), 1164-1169.
dx.doi.org

Aguayo, D.; González-Nilo, F.D.; Chipot, C.
Insight into the Properties of Cardiolipin Containing Bilayers from Molecular Dynamics Simulations, Using a Hybrid All-Atom/United-Atom Force Field
J. Chem. Theory Comput.
  2012, 8 (5), 1765-1773.
dx.doi.org

Liu, Y.; Chipot, C.; Shao, X.; Cai, W.
Edge effects control helical wrapping of carbon nanotubes by polysaccharides
Nanoscale
  2012, 4 (8), 2584-2589.
dx.doi.org

Zou, X.; Ma, W.; Solov'yov, I.A.; Chipot, C.; Schulten, K.
Recognition of methylated DNA through methyl-CpG binding domain proteins
Nucl. Acids Res.
  2012, 40 (6), 2747-2758.
dx.doi.org

Liu, P.; Chipot, C.; Shao, X.; Cai, W.
Solvent-Controlled Shuttling in a Molecular Switch
J. Phys. Chem. C
  2012, 116 (7), 4471-4476.
dx.doi.org

Gaborek, T.J.; Chipot, C.; Madura, J.D.
Conformational Free-Energy Landscapes for a Peptide in Saline Environments
Biophysical Journal
  2012, 103 (12), 2513-2520.
dx.doi.org

Liu, P.; Chipot, C.; Shao, X.; Cai, W.
How Do ?-Cyclodextrins Self-Organize on a Polymer Chain?
J. Phys. Chem. C
  2012, 116 (33), 17913-17918.
dx.doi.org

2011

Gumbart, J.; Chipot, C.; Schulten, K.
Free Energy of Nascent-Chain Folding in the Translocon
Journal of the American Chemical Society
  2011, 133 (19), 7602-7607.
dx.doi.org

Gamini, R.; Sotomayor, M.; Chipot, C.;Schulten, K.
Cytoplasmic Domain Filter Function in the Mechanosensitive Channel of Small Conductance
Biophysical Journal
  2011, 101 (), 80-89.

Lelivre, T.; Chipot, C.
Enhanced sampling of multidimensional free-energy landscapes using adaptive biasing forces
SIAM Journal on Applied Mathematics
  2011,  (), .

Wang, T.; Chipot, C.; Shao, X.; Cai, W.
Structural Characterization of Micelles Formed of Cholesteryl-Functionalized Cyclodextrins
Langmuir
  2011, 27 (1), 91-97.
dx.doi.org

Zúñiga, L.; Márquez, V.; González-Nilo, F. D.; Chipot, C.; Cid, L. P.; Sepúlveda, F. V.; Niemeyer, M. I.
Gating of a pH-Sensitive K2P Potassium Channel by an Electrostatic Effect of Basic Sensor Residues on the Selectivity Filter
PLoS ONEPLoS ONE
  2011, 6 (1), .
dx.doi.org

Liu, Y.; Chipot, C.; Shao, X.; Cai, W.
Free-Energy Landscape of the Helical Wrapping of a Carbon Nanotube by a Polysaccharide
Journal of Physical Chemistry C
  2011, 115 (5), 1851-1856.
dx.doi.org

Luque, F. J.; Dehez, F.; Chipot, C.; Orozco, M.
Polarization effects in molecular interactions
Wiley Interdisciplinary Reviews: Computational Molecular Science
  2011, 1 (), 844-854.
dx.doi.org

Gumbart, J.; Chipot, C.; Schulten, K.
Free-energy cost for translocon-assisted insertion of membrane proteins
Proceedings of the National Academy of Sciences
  2011, 108 (9), 3596-3601.
dx.doi.org

Hsin, J.; LaPointe, L.M.; Kazy, A.; Chipot, C.; Senes, A.; Schulten, K.
Oligomerization State of Photosynthetic Core Complexes Is Correlated with the Dimerization Affinity of a Transmembrane Helix
Journal of the American Chemical Society
  2011, 133 (35), 14071-14081.
dx.doi.org

Liu, Y.; Chipot, C.; Shao, X.; Cai, W.
The effects of 7-dehydrocholesterol on the structural properties of membranes
Physical Biology
  2011, 8 (5), 056005.
dx.doi.org

Sheng Cai, W.; Wang, T.; Zhe Liu, Y.; Liu, P.; Chipot, C.; Guang Shao, X.
Free Energy Calculations for Cyclodextrin Inclusion Complexes
Current Organic Chemistry
  2011, 15 (6), 839-847.
dx.doi.org

2010

Henin, J.; Fiorin, G.; Chipot, C.; Klein, M.L.
Exploring Multidimensional Free Energy Landscapes Using Time-Dependent Biases on Collective Variables
Journal Of Chemical Theory And Computation
  2010, 6 (1), 35-47.
dx.doi.org

Khalfa, A; Tarek, M
On the Antibacterial Action of Cyclic Peptides: Insights from Coarse-Grained MD Simulations
Journal of Physical Chemistry B
  2010, 114 (8), 2676-2684.
dx.doi.org

Kraszewski, S; Tarek, M; Treptow, W; Ramseyer, C
Affinity of C-60 Neat Fullerenes with Membrane Proteins: A Computational Study on Potassium Channels
Acs Nano
  2010, 4 (7), 4158-4164.
dx.doi.org

Delemotte, L.; Treptow, W.; Klein, M. L.; Tarek, M.
Effect of Sensor Domain Mutations on the Properties of Voltage-Gated Ion Channels: Molecular Dynamics Studies of the Potassium Channel Kv1.2
Biophysical JournalBiophysical Journal
  2010, 99 (9), L72-L74.
dx.doi.org

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

Liu, YZ; Chipot, C; Shao, XG; Cai, WS
Solubilizing Carbon Nanotubes through Noncovalent Functionalization. Insight from the Reversible Wrapping of Alginic Acid around a Single-Walled Carbon Nanotube
Journal Of Physical Chemistry B
  2010, 114 (17), 5783-5789.
dx.doi.org

Liu, P; Cai, WS; Chipot, C; Shao, XG
Thermodynamic Insights into the Dynamic Switching of a Cyclodextrin in a Bistable Molecular Shuttle
Journal of Physical Chemistry Letters
  2010, 1 (12), 1776-1780.

Pohorille, A; Jarzynski, C; Chipot, C
Good Practices in Free-Energy Calculations
Journal of Physical Chemistry B
  2010, 114 (32), 10235-10253.
dx.doi.org

Chebil, L.; Chipot, C; Archambault, F; Humeau, C; Engasser, JM; Ghoul, M; Dehez, F
Solubilities Inferred from the Combination of Experiment and Simulation. Case Study of Quercetin in a Variety of Solvents
Journal Of Physical Chemistry B
  2010, 114 (38), 12308-12313.
dx.doi.org

Montserret, R; Saint, N; Vanbelle, C; Salvay, AG; Simorre, JP; Ebel, C; Sapay, N; Renisio, JG; Bockmann, A; Steinmann, E; Pietschmann, T; Dubuisson, J; Chipot, C; Penin, F
NMR Structure and Ion Channel Activity of the p7 Protein from Hepatitis C Virus
Journal Of Biological Chemistry
  2010, 285 (41), 31446-31461.
dx.doi.org

Champagnat, N.; Chipot, C.; Faou, E.
Reconciling alternate methods for the determination of charge distributions: a probabilistic approach to high-dimensional least-squares approximations
Journal of Mathematical ChemistryJ Math Chem
  2010, 49 (1), 296-324.
dx.doi.org

Tarek, M.; Delemotte, L.
Electroporation of lipid membranes. In Advanced Electroporation Techniques in Biology and Medicine Andrei Pakhomov, Damijan Miklavcic and Marko Markov, Editors
  2010,  (), .

Tarek, M.; Delemotte, L.
Water and Membranes: Insights from molecular dynamics simulations. In Water, The Forgotten Biological Molecule. Denis le Bihan and Hidenao Fukuyama, Editors
  2010,  (), .

2009

Cai, W.S.; Sun, T.T.; Liu, P.; Chipot, C.; Shao, X.G.
Inclusion Mechanism of Steroid Drugs into beta-Cyclodextrins. Insights from Free Energy Calculations
Journal Of Physical Chemistry B
  2009, 113 (22), 7836-7843.
dx.doi.org

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

Tobias, D.J.; Sengupta, N.; Tarek, M.
Hydration dynamics of purple membranes
Faraday Discussions
  2009, 141 (), 99-116.
dx.doi.org

Treptow, W.; Tarek, M.; Klein, M.L.
Initial Response of the Potassium Channel Voltage Sensor to a Transmembrane Potential
Journal Of The American Chemical Society
  2009, 131 (6), 2107-+.
dx.doi.org

Hsin, J.; Chipot, C.; Schulten, K.
A Glycophorin A-Like Framework for the Dimerization of Photosynthetic Core Complexes
Journal Of The American Chemical Society
  2009, 131 (47), 17096-+.
dx.doi.org

Chandler, D.E.; Gumbart, J.; Stack, J.D.; Chipot, C.; Schulten, K.
Membrane Curvature Induced by Aggregates of LH2s and Monomeric LH1s
Biophysical Journal
  2009, 97 (11), 2978-2984.
dx.doi.org

Krammer, E.M.; Ravaud, S.; Dehez, F.; Frelet-Barrand, A.; Pebay-Peyroula, E.; Chipot, C.
High-Chloride Concentrations Abolish the Binding of Adenine Nucleotides in the Mitochondrial ADP/ATP Carrier Family
Biophysical Journal
  2009, 97 (10), L25-L27.
dx.doi.org

Archambault, F.; Chipot, C.; Soteras, I.; Luque, F.J.; Schulten, K.; Dehez, F.
Polarizable Intermolecular Potentials for Water and Benzene Interacting with Halide and Metal Ions
Journal Of Chemical Theory And Computation
  2009, 5 (11), 3022-3031.
dx.doi.org

Saint, N.; Montserret, R.; Chipot, C.; Penin, F.
Structural and Functional Analysis of the HCV p7 Protein
Methods in Molecular Biology
  2009,  (), 125-143.
dx.doi.org

De Oliveira, E. B.; Humeau, C.; Chebil, L.; Maia, E. R.; Dehez, F.; Maigret, B.; Ghoul, M.; Engasser, J. M.
A molecular modelling study to rationalize the regioselectivity in acylation of flavonoid glycosides catalyzed by Candida antarctica lipase B
Journal of Molecular Catalysis B-Enzymatic
  2009, 59 (1-3), 96-105.
dx.doi.org

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

Chipot, C.
Molecular dynamics: Observing matter in motion. in Nanoscience: Nanobiotechnology and Nanobiology, Boisseau, P.; Lahmani, M. and ; Houdy, P., Eds.
  2009,  (), .

2008

Henin, J.; Tajkhorshid, E.; Schulten, K.; Chipot, C.
Diffusion of glycerol through Escherichia coli aquaglyceroporin GlpF
Biophysical Journal
  2008, 94 (3), 832-839.
dx.doi.org

Treptow, W.; Marrink, S.J.; Tarek, M.
Gating motions in voltage-gated potassium channels revealed by coarse-grained molecular dynamics simulations
Journal Of Physical Chemistry B
  2008, 112 (11), 3277-3282.
dx.doi.org

Yu, Y.M.; Cai, W.S.; Chipot, C.; Sun, T.T.; Shao, X.G.
Spatial arrangement of alpha-cyclodextrins in a rotaxane. Insights from free-energy calculations
Journal Of Physical Chemistry B
  2008, 112 (17), 5268-5271.
dx.doi.org

Cai, W.; Sun, T.; Shao, X.; Chipot, C.
Can the anomalous aqueous solubility of beta-cyclodextrin be explained by its hydration free energy alone?
Physical Chemistry Chemical Physics
  2008, 10 (22), 3236-3243.
dx.doi.org

Tarek, M.; Tobias, D.J.
The role of protein-solvent hydrogen bond dynamics in the structural relaxation of a protein in glycerol versus water
European Biophysics Journal With Biophysics Letters
  2008, 37 (5), 701-709.
dx.doi.org

Dehez, F.; Pebay-Peyroula, E.; Chipot, C.
Binding of ADP in the mitochondrial ADP/ATP carrier is driven by an electrostatic funnel
Journal Of The American Chemical Society
  2008, 130 (38), 12725-12733.
dx.doi.org

Chipot, C.
Milestones in the Activation of a G Protein-Coupled Receptor. Insights from Molecular-Dynamics Simulations into the Human Cholecystokinin Receptor-1
Journal Of Chemical Theory And Computation
  2008, 4 (12), 2150-2159.
dx.doi.org

Delemotte, L.; Dehez, F.; Treptow, W.; Tarek, M.
Modeling membranes under a transmembrane potential
Journal Of Physical Chemistry BJ. Phys. Chem. B
  2008, 112 (18), 5547-5550.
dx.doi.org

Paciaroni, A.; Orecchini, A.; Cornicchi, E.; Marconi, M.; Petrillo, C.; Haertlein, M.; Moulin, M.; Schober, H.; Tarek, M.; Sacchetti, F.
Fingerprints of amorphous icelike behavior in the vibrational density of states of protein hydration water
Physical Review Letters
  2008, 101 (14), .
dx.doi.org

Dehez, F.; Archambault, F.; Soteras Gutierrez, I.; Javier Luque, F.; Chipot, C.
An ab initio strategy for handling induction phenomena in metal ion complexes
Molecular PhysicsMol. Phys.
  2008, 106 (12), 1685-1696.
dx.doi.org

Pebay-Peyroula, E.; Chipot, C.; Schulten, K.
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
  2008,  (), .

Chipot, C.
Free energy calculations applied to membrane proteins. In Molecular modeling of proteins, Kukol, A., Ed., vol. 443
  2008,  (), 121-144.

2007

Bonnon, C.; Bel, C.; Goutebroze, L.; Maigret, B.; Girault, J.A.; Faivre-Sarrailh, C.
PGY repeats and N-glycans govern the trafficking of paranodin and its selective association with contactin and neurofascin-155
Molecular Biology Of The Cell
  2007, 18 (1), 229-241.
dx.doi.org

Chebil, L.; Humeau, C.; Anthoni, J.; Dehez, F.; Engasser, J.M.; Ghoul, M.
Solubility of flavonoids in organic solvents
Journal Of Chemical And Engineering Data
  2007, 52 (), 1552-1556.
dx.doi.org

Dehez, F.; Tarek, M.; Chipot, C.
Energetics of ion transport in a peptide nanotube
Journal Of Physical Chemistry B
  2007, 111 (36), 10633-10635.
dx.doi.org

Floquet, N.; Richez, C.; Durand, P.; Maigret, B.; Badet, B.; Badet-Denisot, M.A.
Discovering new inhibitors of bacterial glucosamine-6P synthase (GlmS) by docking simulations
Bioorganic & Medicinal Chemistry Letters
  2007, 17 (7), 1966-1970.
dx.doi.org

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

Leroux, V.; Gresh, N.; Liu, W.Q.; Garbay, C.; Maigret, B.
Role of water molecules for binding inhibitors in the SH2 domain of Grb2: A molecular dynamics study
Journal Of Molecular Structure-Theochem
  2007, 806 (1-3), 51-66.
dx.doi.org

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

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

Dehez, F.; Ángyán, J. G.; Gutiérrez, I. S.; Luque, F. J.; Schulten, K.; Chipot, C.
Modeling Induction Phenomena in Intermolecular Interactions with an Ab Initio Force Field
Journal of Chemical Theory and Computation
  2007, 3 (6), 1914-1926.
dx.doi.org

Soteras, I.; Curutchet, C.; Bidon-Chanal, A.; Dehez, F.; Ángyán, J. G.; Orozco, M.; Chipot, C.; Luque, F. J.
Derivation of Distributed Models of Atomic Polarizability for Molecular Simulations
Journal of Chemical Theory and Computation
  2007, 3 (6), 1901-1913.
dx.doi.org

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

2006

Chipot, C.; Tarek, M.
Interaction of a peptide nanotube with a water-membrane interface
Physical Biology
  2006, 3 (1), S20-S25.
dx.doi.org

Henin, J.; Chipot, C.
Hydrogen-bonding patterns of cholesterol in lipid membranes
Chemical Physics Letters
  2006, 425 (4-6), 329-335.
dx.doi.org

Henin, J.; Maigret, B.; Tarek, M.; Escrieut, C.; Fourmy, D.; Chipot, C.
Probing a model of a GPCR/ligand complex in an explicit membrane environment: The human cholecystokinin-1 receptor
Biophysical Journal
  2006, 90 (4), 1232-1240.
dx.doi.org

Henin, J.; Schulten, K.; Chipot, C.
Conformational equilibrium in alanine-rich peptides probed by reversible stretching simulations
Journal Of Physical Chemistry B
  2006, 110 (33), 16718-16723.
dx.doi.org

Sapay, N.; Montserret, R.; Chipot, C.; Brass, V.; Moradpour, D.; Deleage, G.; Penin, F.
NMR structure and molecular dynamics of the in-plane membrane anchor of nonstructural. protein 5A from bovine viral diarrhea virus
Biochemistry
  2006, 45 (7), 2221-2233.
dx.doi.org

Treptow, W.; Tarek, M.
Environment of the gating charges in the Kv1.2 Shaker potassium channel
Biophysical Journal
  2006, 90 (9), L64-L66.
dx.doi.org

Yu, Y.M.; Chipot, C.; Cai, W.S.; Shao, X.G.
Molecular dynamics study of the inclusion of cholesterol into cyclodextrins
Journal Of Physical Chemistry B
  2006, 110 (12), 6372-6378.
dx.doi.org

Henin, J.; Chipot, C.
Hydrogen-bonding patterns of cholesterol in lipid membranes
Chemical Physics Letters
  2006, 425 (4-6), 329-335.

Treptow, W.; Tarek, M.
K+ conduction in the selectivity filter of potassium channels is monitored by the charge distribution along their sequence
Biophysical Journal
  2006, 91 (10), L81-L83.
dx.doi.org

Treptow, W.; Tarek, M.
Molecular restraints in the permeation pathway of ion channels
Biophysical Journal
  2006, 91 (3), L26-L28.
dx.doi.org

2005

Chipot, C.; Rozanska, X.; Dixit, S.B.
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
Journal Of Computer-Aided Molecular Design
  2005, 19 (11), 765-770.
dx.doi.org

Chipot, C.; Henin, J.
Exploring the free-energy landscape of a short peptide using an average force
Journal Of Chemical Physics
  2005, 123 (24), .
dx.doi.org

Dehez, F.; Martins-Costa, M.T.C.; Rinaldi, D.; Millot, C.
Long-range electrostatic interactions in hybrid quantum and molecular mechanical dynamics using a lattice summation approach
Journal Of Chemical Physics
  2005, 122 (23), .
dx.doi.org

Henin, J.; Pohorille, A.; Chipot, C.
Insights into the recognition and association of transmembrane alpha-helices. The free energy of alpha-helix dimerization in glycophorin A
Journal Of The American Chemical Society
  2005, 127 (23), 8478-8484.
dx.doi.org

Henin, M.; Pohorille, A.; Chipot, C.
Insights into the recognition and association of transmembrane alpha-helices. The free energy of alpha-helix dimerization in glycophorin A
Journal Of The American Chemical Society
  2005, 127 (23), 8478-8484.

Phillips, J.C.; Braun, R.; Wang, W.; Gumbart, J.; Tajkhorshid, E.; Villa, E.; Chipot, C.; Skeel, R.D.; Kale, L.; Schulten, K.
Scalable molecular dynamics with NAMD
Journal Of Computational Chemistry
  2005, 26 (16), 1781-1802.
dx.doi.org

Tarek, M.
Membrane electroporation: A molecular dynamics simulation
Biophysical Journal
  2005, 88 (6), 4045-4053.
dx.doi.org

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

Trebbi, B.; Dehez, F.; Fowler, P.W.; Zerbetto, F.
Favorable entropy of aromatic clusters in thermophilic proteins
Journal Of Physical Chemistry B
  2005, 109 (38), 18184-18188.
dx.doi.org

2004

Curtis, J.E.; Tarek, M.; Tobias, D.J.
Methyl group dynamics as a probe of the protein dynamical transition
Journal Of The American Chemical Society
  2004, 126 (49), 15928-15929.
dx.doi.org

Henin, J.; Chipot, C.
Overcoming free energy barriers using unconstrained molecular dynamics simulations
Journal Of Chemical Physics
  2004, 121 (7), 2904-2914.
dx.doi.org

Treptow, W.; Maigret, B.; Chipot, C.; Tarek, M.
Coupled motions between pore and voltage-sensor domains: A model for Shaker B, a voltage-gated potassium channel
Biophysical Journal
  2004, 87 (4), 2365-2379.
dx.doi.org

2003

Chipot, C.
Rational determination of charge distributions for free energy calculations
Journal Of Computational Chemistry
  2003, 24 (4), 409-415.
dx.doi.org

Collet, O.; Chipot, C.
Non-arrhenius behavior in the unfolding of a short, hydrophobic alpha-helix. Complementarity of molecular dynamics and lattice model simulations
Journal Of The American Chemical Society
  2003, 125 (21), 6573-6580.
dx.doi.org

Koubi, L.; Saiz, L.; Tarek, M.; Scharf, D.; Klein, M.L.
Influence of anesthetic and nonimmobilizer molecules on the physical properties of a polyunsaturated lipid bilayer
Journal Of Physical Chemistry B
  2003, 107 (51), 14500-14508.
dx.doi.org

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

Tarek, M.; Neumann, D.A.; Tobias, D.J.
Characterization of sub-nanosecond dynamics of the molten globule state of alpha-lactalbumin using quasielastic neutron scattering and molecular dynamics simulations
Chemical Physics
  2003, 292 (2-3), 435-443.
dx.doi.org

Tarek, M.; Maigret, B.; Chipot, C.
Molecular dynamics investigation of an oriented cyclic peptide nanotube in DMPC bilayers
Biophysical Journal
  2003, 85 (4), 2287-2298.

2002

Bas, D.; Dorison-Duval, D.; Moreau, S.; Bruneau, P.; Chipot, C.
Rational determination of transfer free energies of small drugs across the water-oil interface
Journal Of Medicinal Chemistry
  2002, 45 (1), 151-159.
dx.doi.org

Chipot, C.; Pearlman, D.A.
Free energy calculations. The long and winding gilded road
Molecular Simulation
  2002, 28 (1-2), 1-12.
dx.doi.org

Tarek, M.; Tobias, D.J.
Single-particle and collective dynamics of protein hydration water: A molecular dynamics study
Physical Review Letters
  2002, 89 (27), .
dx.doi.org

2001

Chipot, C.
Insights into the self-assembly of small, organic molecules: Case study of 2,4,6-trichlorophenol
Journal Of Physical Chemistry B
  2001, 105 (25), 5987-5993.
dx.doi.org

Dixit, S.B.; Chipot, C.
Can absolute free energies of association be estimated from molecular mechanical simulations? The biotin-streptavidin system revisited
Journal Of Physical Chemistry A
  2001, 105 (42), 9795-9799.

2000

Couturier, R.; Chipot, C.
Parallel molecular dynamics using OPENMP on a shared memory machine
Computer Physics Communications
  2000, 124 (1), 49-59.

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

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

Rozanska, X.; Chipot, C.
Modeling ion-ion interaction in proteins: A molecular dynamics free energy calculation of the guanidinium-acetate association
Journal Of Chemical Physics
  2000, 112 (22), 9691-9694.

Recent publications

Bignon, E.; Gattuso, H.; Morell, C.; Dehez, F.; Georgakilas, A. G.; Monari, A. & Dumont, E.
Correlation of bistranded clustered abasic DNA lesion processing with structural and dynamic DNA helix distortion.
Nucleic Acids Res.

2016,  (44), 8588-8599.
dx.doi.org

Wang, S.; Zhao, T.; Shao, X.; Chipot, C.; Cai, W.
Complex movements in rotaxanes: Shuttling coupled with conformational transition of cyclodextrins
J. Phys. Chem. C

2016,  (120), 19479-19486.
dx.doi.org

Gattuso, H.; Durand, E.; Bignon, E.; Morell, C.; Georgakilas, A. G.; Dumont, E.; Chipot, C.; Dehez, F.; Monari, A.
Repair rate of clustered abasic DNA lesions by human endonuclease: Molecular bases of sequence specificity
J. Phys. Chem. Lett

2016,  (19), 3760-3765.
dx.doi.org

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

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