C. Chipot

发表

Molecular modeling of protocellular functions.

A. Pohorille, C. Chipot, M. New, 1996, Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing.

Laxmikant V. Kalé, Klaus Schulten, Wei Wang, 2005, J. Comput. Chem..

Overcoming free energy barriers using unconstrained molecular dynamics simulations.

C. Chipot, J. Hénin, 2004, The Journal of chemical physics.

Insights into the recognition and association of transmembrane α-helices. The free energy of α-helix dimerization in glycophorin A

A. Pohorille, C. Chipot, J. Hénin, 2005 .

The development/application of a ‘minimalist’ organic/biochemical molecular mechanic force field using a combination of ab initio calculations and experimental data

A. Pohorille, P. Kollman, C. Chipot, 1997 .

Modeling amino acid side chains. 3. Influence of intra- and intermolecular environment on point charges

H. Scheraga, C. Chipot, J. Ángyán, 1993 .

Cation−π Interactions in Proteins: Can Simple Models Provide an Accurate Description?

Christophe Chipot, Hervé Minoux, C. Chipot, 1999 .

Free energy calculations : theory and applications in chemistry and biology

A. Pohorille, C. Chipot, 2007 .

Binding of ADP in the mitochondrial ADP/ATP carrier is driven by an electrostatic funnel.

Christophe Chipot, François Dehez, Eva Pebay-Peyroula, 2008, Journal of the American Chemical Society.

Potential of Mean Force Calculations: A Multiple-Walker Adaptive Biasing Force Approach

Christophe Chipot, Tony Lelièvre, T. Lelièvre, 2010 .

Folding and translocation of the undecamer of poly-L-leucine across the water-hexane interface. A molecular dynamics study.

A. Pohorille, C. Chipot, 1998, Journal of the American Chemical Society.

Inhibitor Binding Influences the Protonation State of Histidines in SARS-CoV-2 Main Protease

Jerry M. Parks, Jeremy C. Smith, Callum J. Dickson, 2020, bioRxiv.

Solubilizing carbon nanotubes through noncovalent functionalization. Insight from the reversible wrapping of alginic acid around a single-walled carbon nanotube.

C. Chipot, W. Cai, X. Shao, 2010, The journal of physical chemistry. B.

Diffusion of glycerol through Escherichia coli aquaglyceroporin GlpF.

Klaus Schulten, Christophe Chipot, Jérôme Hénin, 2008, Biophysical journal.

Thermodynamics of Deca-alanine Folding in Water

Christophe Chipot, James C. Gumbart, Anthony Hazel, 2014, Journal of chemical theory and computation.

Hydrogen-bonding patterns of cholesterol in lipid membranes

C. Chipot, J. Hénin, 2006 .

Exploring Multidimensional Free Energy Landscapes Using Time-Dependent Biases on Collective Variables.

Christophe Chipot, Giacomo Fiorin, Michael L Klein, 2010, Journal of chemical theory and computation.

Permeability of a Fluid Lipid Bilayer to Short-Chain Alcohols from First Principles.

K. Schulten, C. Chipot, J. Comer, 2017, Journal of chemical theory and computation.

What causes tumbling of altro-α-CD derivatives? Insight from computer simulations

C. Chipot, W. Cai, X. Shao, 2015 .

Molecular dynamics investigation of an oriented cyclic peptide nanotube in DMPC bilayers.

Christophe Chipot, Bernard Maigret, Mounir Tarek, 2003, Biophysical journal.

Reconciling alternate methods for the determination of charge distributions: a probabilistic approach to high-dimensional least-squares approximations

E. Faou, C. Chipot, Nicolas Champagnat, 2010, 1006.4996.

Cytoplasmic domain filter function in the mechanosensitive channel of small conductance.

K. Schulten, C. Chipot, M. Sotomayor, 2011, Biophysical journal.

Numerical methods for molecular dynamics simulations of biological systems

C. Chipot, 2010 .

Transferable net atomic charges from a distributed multipole analysis for the description of electrostatic properties: a case study of saturated hydrocarbons

György G. Ferenczy, Christophe Chipot, Harold A. Scheraga, 1993 .

New Coarse Variables for the Accurate Determination of Standard Binding Free Energies.

C. Chipot, W. Cai, B. Roux, 2017, Journal of chemical theory and computation.

Solubilities inferred from the combination of experiment and simulation. Case study of quercetin in a variety of solvents.

C. Chipot, M. Ghoul, J. Engasser, 2010, The journal of physical chemistry. B.

Molecular dynamics free energy simulations: Influence of the truncation of long‐range nonbonded electrostatic interactions on free energy calculations of polar molecules

P. Kollman, C. Chipot, B. Maigret, 1994 .

Free energy of nascent-chain folding in the translocon.

K. Schulten, C. Chipot, J. Gumbart, 2011, Journal of the American Chemical Society.

Cryo-EM and MD infer water-mediated proton transport and autoinhibition mechanisms of Vo complex

W. Chiu, C. Chipot, A. Singharoy, 2020, Science Advances.

Charge Distribution Calculations: Alternative Approaches

C. Chipot, W. Cornell, 2002 .

Structural Basis for Broad HIV-1 Neutralization by the MPER-Specific Human Broadly Neutralizing Antibody LN01

C. Chipot, D. Montefiori, W. Weissenhorn, 2019, Cell host & microbe.

Structural and energetic study of cation-π-cation interactions in proteins.

C. Chipot, J. Gelpí, F. Dehez, 2017, Physical chemistry chemical physics : PCCP.

Simulation-Based Approaches for Determining Membrane Permeability of Small Compounds

Yi Wang, Robert V. Swift, Rommie E. Amaro, 2016, J. Chem. Inf. Model..

Exploring the free-energy landscape of a short peptide using an average force.

Christophe Chipot, Jérôme Hénin, C. Chipot, 2005, The Journal of chemical physics.

Avoiding non-equilibrium effects in adaptive biasing force calculations

C. Chipot, W. Cai, X. Shao, 2020 .

How Does the Solvent Modulate Shuttling in a Pillararene/Imidazolium [2]Rotaxane? Insights from Free Energy Calculations

C. Chipot, W. Cai, X. Shao, 2016 .

From material science to avant-garde cuisine. The art of shaping liquids into spheres.

C. Chipot, W. Cai, X. Shao, 2014, The journal of physical chemistry. B.

Conformational free-energy landscapes for a peptide in saline environments.

C. Chipot, J. Madura, Timothy J. Gaborek, 2012, Biophysical journal.

Solvent-Controlled Shuttling in a Molecular Switch

C. Chipot, W. Cai, X. Shao, 2012 .

Free energy calculations applied to membrane proteins.

C. Chipot, 2008, Methods in molecular biology.

Non-arrhenius behavior in the unfolding of a short, hydrophobic alpha-helix. Complementarity of molecular dynamics and lattice model simulations.

C. Chipot, O. Collet, 2003, Journal of the American Chemical Society.

Machine Learning Reveals the Critical Interactions for SARS-CoV-2 Spike Protein Binding to ACE2

Jerry M. Parks, C. Chipot, J. Gumbart, 2021, Biophysical Journal.

Decrypting protein insertion through the translocon with free-energy calculations.

C. Chipot, J. Gumbart, 2016, Biochimica et biophysica acta.

Modeling Lipid Membranes

C. Chipot, M. Klein, M. Tarek, 2005 .

Complexation mechanism of cucurbit[6]uril with hexamethylene diammonium cations in saline solution.

C. Chipot, Peng Liu, W. Cai, 2014, Physical chemistry chemical physics : PCCP.

Accurate Estimation of the Standard Binding Free Energy of Netropsin with DNA

C. Chipot, W. Cai, F. Dehez, 2018, Molecules.

Conserved methionine dictates substrate preference in Nramp-family divalent metal transporters

K. Schulten, C. Chipot, A. Bozzi, 2016, Proceedings of the National Academy of Sciences.

Thermodynamics of DNA: sensitizer recognition. Characterizing binding motifs with all-atom simulations.

C. Chipot, F. Dehez, É. Dumont, 2016, Physical chemistry chemical physics : PCCP.

Assessing the physiological relevance of alternate architectures of the p7 protein of hepatitis C virus in different environments.

C. Chipot, F. Penin, F. Dehez, 2016, Bioorganic & medicinal chemistry.

Why do the structural properties of complexes formed by glucans and carbon nanotubes differ so much

C. Chipot, W. Cai, X. Shao, 2015 .

Mitochondrial ADP/ATP Carrier in Dodecylphosphocholine Binds Cardiolipins with Non-native Affinity

C. Chipot, P. Schanda, F. Dehez, 2017, Biophysical journal.

Molecular Mechanism of Processive 3' to 5' RNA Translocation in the Active Subunit of the RNA Exosome Complex.

K. Schulten, C. Chipot, E. Conti, 2016, Journal of the American Chemical Society.

pH-Controlled Fluorescence Probes for Rotaxane Isomerization

C. Chipot, W. Cai, X. Shao, 2019, The Journal of Physical Chemistry C.

Distributed polarizabilities derived from induction energies: A finite perturbation approach

C. Chipot, J. Ángyán, F. Dehez, 2000 .

Numerical methods in molecular dynamics, or what is a metastable stochastic process ?

C. Chipot, D. Aristoff, N. Chopin, 2014 .

Structural Basis for Broad HIV-1 Neutralization by a Novel MPER-Specific Human Broadly Neutralizing Antibody

C. Chipot, D. Montefiori, W. Weissenhorn, 2019, SSRN Electronic Journal.

The Binding of Palonosetron and Other Antiemetic Drugs to the Serotonin 5-HT3 Receptor.

C. Chipot, W. Cai, J. Neyton, 2020, Structure.

The binding of palonosetron and other antiemetic drugs to the serotonin 5-HT3 receptor

C. Chipot, W. Cai, J. Neyton, 2020, bioRxiv.

Triggering Tautomerization of Curcumin by Confinement into Liposomes

C. Chipot, F. Dehez, M. Girardon, 2019, ChemPhotoChem.

Accurate Description of Solvent-Exposed Salt Bridges with a Non-polarizable Force Field Incorporating Solvent Effects

C. Chipot, W. Cai, Haohao Fu, 2022, J. Chem. Inf. Model..

How Detergent Impacts Membrane Proteins: Atomic-Level Views of Mitochondrial Carriers in Dodecylphosphocholine

C. Chipot, Rémy Sounier, P. Schanda, 2018, The journal of physical chemistry letters.

When the Dust Has Settled: Calculation of Binding Affinities from First Principles for SARS-CoV-2 Variants with Quantitative Accuracy

C. Chipot, J. Gumbart, Haochuan Chen, 2022, Journal of chemical theory and computation.

Molecular Basis of DNA Packaging in Bacteria Revealed by All-Atoms Molecular Dynamic Simulations: The case of histone like proteins in Borrelia burgdoferi.

C. Chipot, F. Dehez, Cécilia Hognon, 2021 .

Perforin-2 clockwise hand-over-hand pre-pore to pore transition mechanism

C. Chipot, J. Dittman, S. Scheuring, 2022, Nature Communications.

Conformational equilibrium in alanine-rich peptides probed by reversible stretching simulations.

K. Schulten, C. Chipot, J. Hénin, 2006, The journal of physical chemistry. B.

Hazardous Shortcuts in Standard Binding Free Energy Calculations.

C. Chipot, Haochuan Chen, Marharyta Blazhynska, 2022, The journal of physical chemistry letters.

Modeling Lipid Membranes

C. Chipot, M. Klein, M. Tarek, 2005 .

Free-Energy Landscape of Stepwise, Directional Motion in Multiple Molecular Switches

C. Chipot, W. Cai, X. Shao, 2020 .

Conformational changes of DNA induced by a trans-azobenzene derivative via non-covalent interactions.

C. Chipot, W. Cai, X. Shao, 2018, Physical chemistry chemical physics : PCCP.

Dynamics and interactions of ADP/ATP transporter AAC3 in DPC detergent are not functionally relevant

C. Chipot, P. Schanda, F. Dehez, 2018, bioRxiv.

Repair Rate of Clustered Abasic DNA Lesions by Human Endonuclease: Molecular Bases of Sequence Specificity.

C. Chipot, E. Bignon, A. Georgakilas, 2016, The journal of physical chemistry letters.

Committor-Consistent Variational String Method.

C. Chipot, Benoı T Roux, Ziwei He, 2022, The journal of physical chemistry letters.

Binding properties of the quaternary assembly protein SPAG1.

C. Chipot, M. Chagot, F. Dehez, 2019, The Biochemical journal.

Modeling induction phenomena in amino acid cation–$$\pi $$π interactions

C. Chipot, B. Roux, F. Dehez, 2018, Theoretical Chemistry Accounts.

Complex Movements in Rotaxanes: Shuttling Coupled with Conformational Transition of Cyclodextrins

C. Chipot, W. Cai, X. Shao, 2016 .

Galvani Offset Potential and Constant-pH Simulations of Membrane Proteins

C. Chipot, S. Kellenberger, Olivier Bignucolo, 2022, The journal of physical chemistry. B.

Rotational Mechanism Model of the Bacterial V1 Motor Based on Structural and Computational Analyses

C. Chipot, M. Ikeguchi, A. Singharoy, 2019, Front. Physiol..

Enhancing sampling with free-energy calculations.

C. Chipot, Haochuan Chen, 2022, Current opinion in structural biology.

Dynamics and interactions of AAC3 in DPC are not functionally relevant

C. Chipot, P. Schanda, F. Dehez, 2018, Nature Structural & Molecular Biology.

Frontiers in High-Performance, Large-Scale Molecular Dynamics. 35 Years of Molecular-Dynamics Simulations of Biological Systems

C. Chipot, Cai Wensheng, 2013 .

Structural analysis of the KGD sequence loop of barbourin, an αIIbβ3-specific disintegrin

Christophe Chipot, David Brown, Bernard Maigret, 2000, J. Comput. Aided Mol. Des..

Structural characterization of micelles formed of cholesteryl-functionalized cyclodextrins.

Christophe Chipot, Xueguang Shao, Wensheng Cai, 2011, Langmuir : the ACS journal of surfaces and colloids.

Can the anomalous aqueous solubility of beta-cyclodextrin be explained by its hydration free energy alone?

C. Chipot, W. Cai, X. Shao, 2008, Physical chemistry chemical physics : PCCP.

Threading or Tumbling? Insight into the Self-Inclusion Mechanism of an altro-α-Cyclodextrin Derivative

C. Chipot, W. Cai, X. Shao, 2014 .

How Do α-Cyclodextrins Self-Organize on a Polymer Chain?

C. Chipot, W. Cai, X. Shao, 2012 .

Molecular dynamics study of the inclusion of cholesterol into cyclodextrins.

Christophe Chipot, Xueguang Shao, Wensheng Cai, 2006, The journal of physical chemistry. B.

Early events in the folding of an amphipathic peptide: A multinanosecond molecular dynamics study

A. Pohorille, C. Chipot, B. Maigret, 1999, Proteins.

A Multi-Nanosecond Molecular Dynamics Study

Christophe Chipot, Andrew Pohorille, Bernard Maigret, 1999 .

Unveiling the Underlying Mechanism for Compression and Decompression Strokes of a Molecular Engine

C. Chipot, W. Cai, X. Shao, 2014 .

Water-Controlled Switching in Rotaxanes

C. Chipot, W. Cai, X. Shao, 2018 .

Cooperative Recruitment of Amphotericin B Mediated by a Cyclodextrin Dimer

C. Chipot, W. Cai, X. Shao, 2014 .

Cyclodextrin-Mediated Recruitment and Delivery of Amphotericin B

C. Chipot, W. Cai, X. Shao, 2013 .

Methodology for the Simulation of Molecular Motors at Different Scales.

Christophe Chipot, Abhishek Singharoy, C. Chipot, 2017, The journal of physical chemistry. B.

Enthalpy-Entropy Interplay in π-Stacking Interaction of Benzene Dimer in Water.

C. Chipot, Hyungjun Kim, F. Dehez, 2019, Journal of chemical theory and computation.

Molecular Dynamics Potential of Mean Force Calculations: A Study of the Toluene−Ammonium π-Cation Interactions

Peter A. Kollman, Christophe Chipot, David A. Pearlman, 1996 .

Coupled motions between pore and voltage-sensor domains: a model for Shaker B, a voltage-gated potassium channel.

C. Chipot, B. Maigret, M. Tarek, 2004, Biophysical journal.

The substrate specificity of the human ADP/ATP carrier AAC1

C. Chipot, Eva-Maria Krammer, F. Dehez, 2013, Molecular membrane biology.

Scalable molecular dynamics on CPU and GPU architectures with NAMD.

Yi Wang, Aleksei Aksimentiev, Klaus Schulten, 2020, The Journal of chemical physics.

Dangerous liaisons between detergents and membrane proteins. The case of mitochondrial uncoupling protein 2.

C. Chipot, B. Miroux, M. Zoonens, 2013, Journal of the American Chemical Society.

The Mechanism of Action of Hepatitis B Virus Capsid Assembly Modulators Can Be Predicted from Binding to Early Assembly Intermediates.

C. Chipot, R. Schinazi, J. Gumbart, 2022, Journal of medicinal chemistry.

Critical interactions for SARS-CoV-2 spike protein binding to ACE2 identified by machine learning

Jerry M. Parks, C. Chipot, J. Gumbart, 2021, bioRxiv.

FREE ENERGY CALCULATIONS OF WATSON-CRICK BASE PAIRING IN AQUEOUS SOLUTION

C. Chipot, R. Lavery, C. Chipot, 1999 .

Recognition of methylated DNA through methyl-CpG binding domain proteins

K. Schulten, C. Chipot, X. Zou, 2011, Nucleic acids research.

Oligomerization state of photosynthetic core complexes is correlated with the dimerization affinity of a transmembrane helix.

Klaus Schulten, Christophe Chipot, Alessandro Senes, 2011, Journal of the American Chemical Society.

Chapter 13 – Interactions of Small Molecules and Peptides with Membranes

A. Pohorille, C. Chipot, M. New, 1999 .

Molecular Bases of DNA Packaging in Bacteria Revealed by All-Atom Molecular Dynamics Simulations: The Case of Histone-Like Proteins in Borrelia burgdorferi.

C. Chipot, F. Dehez, Cécilia Hognon, 2019, The journal of physical chemistry letters.

Conformational transitions of the serotonin 5-HT3 receptor

C. Chipot, P. Corringer, J. Neyton, 2018, Nature.

Targeting G-quadruplexes with Organic Dyes: Chelerythrine–DNA Binding Elucidated by Combining Molecular Modeling and Optical Spectroscopy

C. Chipot, B. Keppler, F. Dehez, 2019, Antioxidants.

Changes in Microenvironment Modulate the B- to A-DNA Transition

Haohao Fu, Christophe Chipot, Xueguang Shao, 2019, J. Chem. Inf. Model..

Impaired transport of nucleotides in a mitochondrial carrier explains severe human genetic diseases.

C. Chipot, F. Dehez, A. Bidon-Chanal, 2012, ACS chemical biology.

Extended Adaptive Biasing Force Algorithm. An On-the-Fly Implementation for Accurate Free-Energy Calculations.

Haohao Fu, Christophe Chipot, Xueguang Shao, 2016, Journal of chemical theory and computation.

The Adaptive Biasing Force Method: Everything You Always Wanted To Know but Were Afraid To Ask

Christophe Chipot, Jeffrey Comer, Andrew Pohorille, 2014, The journal of physical chemistry. B.

Free Energy Calculations

Christophe Chipot, Andrew Pohorille, A. Pohorille, 2008 .

Good practices in free-energy calculations.

Christophe Chipot, Andrew Pohorille, Christopher Jarzynski, 2010, The journal of physical chemistry. B.

Perturbations of Native Membrane Protein Structure in Alkyl Phosphocholine Detergents: A Critical Assessment of NMR and Biophysical Studies

C. Chipot, P. Schanda, G. Veglia, 2018, Chemical reviews.

Chemomechanical Coupling in Hexameric Protein-Protein Interfaces Harnesses Energy within V-Type ATPases.

K. Schulten, C. Chipot, A. Singharoy, 2017, Journal of the American Chemical Society.

Hepatitis C virus sequence divergence preserves p7 viroporin structural and dynamic features

C. Chipot, J. Schnell, N. Zitzmann, 2019, Scientific Reports.

The p7 Protein of Hepatitis C Virus Forms Structurally Plastic, Minimalist Ion Channels

Klaus Schulten, Christophe Chipot, François Penin, 2012, PLoS Comput. Biol..

NMR Structure and Ion Channel Activity of the p7 Protein from Hepatitis C Virus*

C. Chipot, F. Penin, J. Dubuisson, 2010, The Journal of Biological Chemistry.

Finding an Optimal Pathway on a Multidimensional Free-Energy Landscape

Haohao Fu, Xueguang Shao, Haochuan Chen, 2020, J. Chem. Inf. Model..

Taming Rugged Free Energy Landscapes Using an Average Force.

C. Chipot, W. Cai, X. Shao, 2019, Accounts of chemical research.

Inhibitor binding influences the protonation states of histidines in SARS-CoV-2 main protease

Callum J. Dickson, C. Chipot, J. Gumbart, 2020, Chemical science.

Cation-π interactions and their functional roles in membrane proteins.

C. Chipot, E. Tajkhorshid, C. Ahern, 2021, Journal of molecular biology.

Concentrations of anesthetics across the water-membrane interface; the Meyer-Overton hypothesis revisited.

A. Pohorille, C. Chipot, M. New, 1998, Toxicology letters.

Conformational equilibria of terminally blocked single amino acids at the water-hexane interface. A molecular dynamics study.

A. Pohorille, C. Chipot, C Chipot, 1998, The journal of physical chemistry. B.

Interactions of anesthetics with the water-hexane interface. A molecular dynamics study.

A. Pohorille, C. Chipot, M. Wilson, 1997, The journal of physical chemistry. B.

Membrane Peptides and their Role in Protobiological Evolution

Michael A. Wilson, A. Pohorille, C. Chipot, 2003, Origins of life and evolution of the biosphere.

Calculation of Lipid-Bilayer Permeabilities Using an Average Force.

K. Schulten, C. Chipot, J. Comer, 2014, Journal of chemical theory and computation.

A Lysine Mutation of the Claw-Arm-Like Loop Accelerates Catalysis by Cellobiohydrolases.

C. Chipot, W. Cai, X. Shao, 2019, Journal of the American Chemical Society.

Modeling lipid membranes Modeling lipid membranes

C. Chipot, M. Tarek, 2004 .

Enhanced Sampling of Multidimensional Free-Energy Landscapes Using Adaptive Biasing Forces

Christophe Chipot, Tony Lelièvre, T. Lelièvre, 2010, SIAM J. Appl. Math..

Continuing challenges in the parametrization of intermolecular force fields. Towards an accurate description of electrostatic and induction terms

Christophe Chipot, János G. Ángyán, C. Chipot, 2005 .

Sonoporation at Small and Large Length Scales: Effect of Cavitation Bubble Collapse on Membranes.

Haohao Fu, Christophe Chipot, Jeffrey Comer, 2015, The journal of physical chemistry letters.

Standard binding free energies from computer simulations: What is the best strategy?

Christophe Chipot, Benoît Roux, James C Gumbart, 2013, Journal of chemical theory and computation.

NMR structure and molecular dynamics of the in-plane membrane anchor of nonstructural protein 5A from bovine viral diarrhea virus.

Volker Brass, Christophe Chipot, Darius Moradpour, 2006, Biochemistry.

A Toolkit for the Analysis of Free-Energy Perturbation Calculations.

Peng Liu, Christophe Chipot, Wensheng Cai, 2012, Journal of chemical theory and computation.

Enzyme-mimetic self-catalyzed polymerization of polypeptide helices

C. Chipot, Yao Lin, Lingyang Zhu, 2019, Nature Communications.

Free Energy Calculations. The Long and Winding Gilded Road

Christophe Chipot, David A. Pearlman, C. Chipot, 2002 .

Modeling ion-ion interaction in proteins: A molecular dynamics free energy calculation of the guanidinium-acetate association

Christophe Chipot, Xavier Rozanska, C. Chipot, 2000 .

Chasing collective variables using temporal data-driven strategies

C. Chipot, Haochuan Chen, 2023, QRB Discovery.

Zooming across the Free-Energy Landscape: Shaving Barriers, and Flooding Valleys.

Hong Zhang, Haohao Fu, Christophe Chipot, 2018, The journal of physical chemistry letters.

ELF: An Extended-Lagrangian Free Energy Calculation Module for Multiple Molecular Dynamics Engines

Haohao Fu, Christophe Chipot, Xueguang Shao, 2018, J. Chem. Inf. Model..

Atoms to Phenotypes: Molecular Design Principles of Cellular Energy Metabolism

K. Schulten, J. E. Stone, C. Chipot, 2019, Cell.

Membrane curvature induced by aggregates of LH2s and monomeric LH1s.

Danielle E. Chandler, K. Schulten, C. Chipot, 2009, Biophysical journal.

Benzene Dimer: A Good Model for π−π Interactions in Proteins? A Comparison between the Benzene and the Toluene Dimers in the Gas Phase and in an Aqueous Solution

Peter A. Kollman, Christophe Chipot, Bernard Maigret, 1996 .

Annexin-V stabilizes membrane defects by inducing lipid phase transition

C. Chipot, S. Scheuring, Yi-Chih Lin, 2020, Nature Communications.

Standard Binding Free Energy and Membrane Desorption Mechanism for a Phospholipase C

C. Chipot, N. Reuter, A. Gershenson, 2021, J. Chem. Inf. Model..

Mechanism of the allosteric activation of the ClpP protease machinery by substrates and active-site inhibitors

Diego F. Gauto, C. Chipot, P. Schanda, 2019, Science Advances.

Tuning Proton Transfer Thermodynamics in SARS-CoV-2 Main Protease: Implications for Catalysis and Inhibitor Design

Jeremy C. Smith, C. Chipot, J. Gumbart, 2021, The journal of physical chemistry letters.

Alternative approaches to potential of mean force calculations: Free energy perturbation versus thermodynamic integration. Case study of some representative nonpolar interactions

Peter A. Kollman, Christophe Chipot, David A. Pearlman, 1996, Journal of Computational Chemistry.

Applications of free energy calculations to chemistry and biology

Vijay S. Pande, Thomas Simonson, Christophe Chipot, 2007 .

Free Energy Calculations in Biological Systems. How Useful Are They in Practice

Christophe Chipot, C. Chipot, 2006 .

Molecular Dynamics Free Energy Perturbation Calculations: Influence of Nonbonded Parameters on the Free Energy of Hydration of Charged and Neutral Species

P. Kollman, C. Chipot, B. Maigret, 1994 .

Self-assembly of chlorophenols in water.

C. Chipot, A. Gulik, M. Rogalski, 1999, Proceedings of the National Academy of Sciences of the United States of America.

Alternative approaches to potential of mean force calculations: Free energy perturbation versus thermodynamic integration. Case study of some representative nonpolar interactions

Peter A. Kollman, Christophe Chipot, David A. Pearlman, 1996, J. Comput. Chem..

Effect of Polarizability on the Potential of Mean Force of Two Cations. The Guanidinium−Guanidinium Ion Pair in Water

C. Chipot, J. Ángyán, G. Jansen, 1997 .

Annexin-V stabilizes membrane defects by inducing lipid phase transition

C. Chipot, S. Scheuring, Yi-Chih Lin, 2020, Nature Communications.

Multiple-Replica Strategies for Free-Energy Calculations in NAMD: Multiple-Walker Adaptive Biasing Force and Walker Selection Rules.

Klaus Schulten, James C. Phillips, Christophe Chipot, 2014, Journal of chemical theory and computation.

Structure, substrate binding and symmetry of the mitochondrial ADP/ATP carrier in its matrix-open state.

C. Chipot, F. Dehez, J. Ruprecht, 2021, Biophysical journal.

Transition Pathway for Activation of Ligand-Gated Ion Channels and the Role of Cholesterol

C. Chipot, E. Tajkhorshid, Sunny Hwang, 2020, Biophysical Journal.

Structure of HIV-1 gp41 with its membrane anchors targeted by neutralizing antibodies

A. Trkola, C. Chipot, W. Weissenhorn, 2020, bioRxiv.

OPEP: A tool for the optimal partitioning of electric properties

Claude Millot, Christophe Chipot, François Dehez, 2003, J. Comput. Chem..

Derivation of Distributed Models of Atomic Polarizability for Molecular Simulations.

Christophe Chipot, Modesto Orozco, Carles Curutchet, 2007, Journal of chemical theory and computation.

Fast and accurate determination of induction energies: reduction of topologically distributed polarizability models

Claude Millot, Christophe Chipot, François Dehez, 2001 .

Fast evaluation of induction energies: a second-order perturbation theory approach

F. Javier Luque, Christophe Chipot, F. J. Luque, 2000 .

Statistical analysis of distributed multipoles derived from molecular electrostatic potentials

C. Chipot, J. Ángyán, C. Millot, 1998 .

Frontiers in free‐energy calculations of biological systems

Christophe Chipot, C. Chipot, 2014 .

Efficient determination of protein-protein standard binding free energies from first principles.

Christophe Chipot, Benoît Roux, James C Gumbart, 2013, Journal of chemical theory and computation.

MLCV: Bridging Machine-Learning-Based Dimensionality Reduction and Free-Energy Calculation

C. Chipot, W. Cai, Haochuan Chen, 2021, J. Chem. Inf. Model..

Correlation of membrane protein conformational and functional dynamics

Raghavendar Reddy Sanganna Gari, C. Chipot, S. Scheuring, 2021, Nature Communications.

A glycophorin A-like framework for the dimerization of photosynthetic core complexes.

Klaus Schulten, Christophe Chipot, Jen Hsin, 2009, Journal of the American Chemical Society.

Conformational transitions of the serotonin 5-HT3 receptor

Christophe Chipot, François Dehez, Pierre-Jean Corringer, 2018, Nature.

Curvature of Buckybowl Corannulene Enhances Its Binding to Proteins

C. Chipot, W. Cai, X. Shao, 2019, The Journal of Physical Chemistry C.

NAMD Version 2.4

James C. Phillips, C. Chipot, A. Gursoy, 2002 .

Large-scale molecular dynamics of a G protein-coupled receptor, the human 5-HT4 serotonin receptor, in a lipid bilayer

C. Chipot, B. Maigret, M. Tarek, 2007 .

Milestones in the Activation of a G Protein-Coupled Receptor. Insights from Molecular-Dynamics Simulations into the Human Cholecystokinin Receptor-1.

Christophe Chipot, C. Chipot, 2008, Journal of chemical theory and computation.

Accurate determination of protein:ligand standard binding free energies from molecular dynamics simulations

C. Chipot, W. Cai, J. Gumbart, 2022, Nature Protocols.

Boosting Free-Energy Perturbation Calculations with GPU-Accelerated NAMD

David Joseph Hardy, David J. Hardy, Haochuan Chen, 2020, J. Chem. Inf. Model..

Calculating Free Energy Differences Using Perturbation Theory

Christophe Chipot, Andrew Pohorille, A. Pohorille, 2007 .

Constant-pH Molecular Dynamics Simulations for Large Biomolecular Systems.

Klaus Schulten, James C. Phillips, Sunhwan Jo, 2017, Journal of chemical theory and computation.

BFEE: A User-Friendly Graphical Interface Facilitating Absolute Binding Free-Energy Calculations

Haohao Fu, Christophe Chipot, Xueguang Shao, 2018, J. Chem. Inf. Model..

Molecular Basis of Drug Resistance in A/H1N1 Virus

Klaus Schulten, Fernando D. González Nilo, Ariela Vergara Jaque, 2012, J. Chem. Inf. Model..

Tuning proton transfer thermodynamics in SARS-Cov-2 main protease: implications for catalysis and inhibitor design

Jeremy C. Smith, C. Chipot, J. Gumbart, 2020, ChemRxiv : the preprint server for chemistry.

Calculating Position-Dependent Diffusivity in Biased Molecular Dynamics Simulations.

Christophe Chipot, Jeffrey Comer, C. Chipot, 2013, Journal of chemical theory and computation.

Charge transfer and chemo-mechanical coupling in respiratory complex I.

Chun Kit Chan, C. Chipot, M. Gunner, 2020, Journal of the American Chemical Society.

AlaScan: A Graphical User Interface for Alanine Scanning Free-Energy Calculations

Christophe Chipot, François Dehez, Ramadoss Vijayaraj, 2016, J. Chem. Inf. Model..

Inclusion mechanism of steroid drugs into beta-cyclodextrins. Insights from free energy calculations.

Peng Liu, Christophe Chipot, Xueguang Shao, 2009, The journal of physical chemistry. B.

Achieving ergodic sampling using replica-exchange free-energy calculations

Christophe Chipot, Benoît Roux, Jeffrey Comer, 2014 .

Molecular Dynamics. Observing Matter in Motion

C. Chipot, C. Chipot, 2009 .

Computing Relative Binding Affinity of Ligands to Receptor: An Effective Hybrid Single-Dual-Topology Free-Energy Perturbation Approach in NAMD

Wei Jiang, Benoît Roux, Christophe Chipot, 2019, J. Chem. Inf. Model..

α-Helix Unwinding as Force Buffer in Spectrins.

C. Chipot, F. Rico, S. Scheuring, 2018, ACS nano.

Addressing Polarization Phenomena in Molecular Machines Containing Transition Metal Ions with an Additive Force Field.

C. Chipot, W. Cai, X. Shao, 2019, Journal of chemical theory and computation.

New Algorithms for Macromolecular Simulation

Tamar Schlick, Benedict Leimkuhler, Robert D. Skeel, 2006 .

Modeling Induction Phenomena in Intermolecular Interactions with an Ab Initio Force Field.

K. Schulten, C. Chipot, J. Ángyán, 2007, Journal of chemical theory and computation.

Conformational transitions and ligand-binding to a muscle-type nicotinic acetylcholine receptor

C. Chipot, J. Steyaert, J. Baenziger, 2022, Neuron.

Free-Energy Landscape of the Helical Wrapping of a Carbon Nanotube by a Polysaccharide

C. Chipot, W. Cai, X. Shao, 2011 .

Insights into the recognition and association of transmembrane alpha-helices. The free energy of alpha-helix dimerization in glycophorin A.

A. Pohorille, C. Chipot, J. Hénin, 2005, Journal of the American Chemical Society.

Discovering Reaction Pathways, Slow Variables, and Committor Probabilities with Machine Learning.

C. Chipot, Haochuan Chen, Benoı T Roux, 2023, Journal of chemical theory and computation.

Subdiffusion in Membrane Permeation of Small Molecules

C. Chipot, J. Comer, 2016, Scientific Reports.

Probing a model of a GPCR/ligand complex in an explicit membrane environment: the human cholecystokinin-1 receptor.

Christophe Chipot, Jérôme Hénin, Bernard Maigret, 2006, Biophysical journal.

Predictions from First-Principles of Membrane Permeability to Small Molecules: How Useful Are They in Practice?

C. Chipot, 2023, J. Chem. Inf. Model..

Interaction of alcohols and anesthetics with the water-hexane interface: A molecular dynamics study

Michael A. Wilson, A. Pohorille, C. Chipot, 1997 .

Proton Transfer in the Mono- and the Dihydrated Complexes of HF and HCl: An MP2/6-31+G ab Initio Study in the Self-Consistent Reaction Field Model of Solvation

C. Chipot, J. Rivail, L. Gorb, 1994 .

Biophysics at the dawn of exascale computers.

C. Chipot, A. Singharoy, Alberto Perez, 2023, Biophysical journal.

Accurate Description of Cation-π Interactions in Proteins with a Non-Polarizable Force Field at no Additional Cost.

C. Chipot, W. Cai, X. Shao, 2020, Journal of chemical theory and computation.

Polarizable intermolecular potentials for water and benzene interacting with halide and metal ions.

Klaus Schulten, Christophe Chipot, F. J. Luque, 2009, Journal of chemical theory and computation.

Insight into the Properties of Cardiolipin Containing Bilayers from Molecular Dynamics Simulations, Using a Hybrid All-Atom/United-Atom Force Field.

Christophe Chipot, Daniel Aguayo, C. Chipot, 2012, Journal of chemical theory and computation.

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, Surjit B. Dixit, Xavier Rozanska, 2005, J. Comput. Aided Mol. Des..

Polarization effects in molecular interactions

F. Javier Luque, Christophe Chipot, F. J. Luque, 2011 .

Rational determination of charge distributions for free energy calculations

Christophe Chipot, C. Chipot, 2003, J. Comput. Chem..

The Extended Generalized Adaptive Biasing Force Algorithm for Multidimensional Free-Energy Calculations.

Tanfeng Zhao, Haohao Fu, Christophe Chipot, 2017, Journal of chemical theory and computation.

Improving Speed and Affordability without Compromising Accuracy: Standard Binding Free-Energy Calculations Using an Enhanced Sampling Algorithm, Multiple-Time Stepping, and Hydrogen Mass Repartitioning.

C. Chipot, Haochuan Chen, Marharyta Blazhynska, 2023, Journal of chemical theory and computation.

Achieving Accurate Standard Protein-Protein Binding Free Energy Calculations through the Geometrical Route and Ergodic Sampling

C. Chipot, W. Cai, Haohao Fu, 2023, J. Chem. Inf. Model..

BFEE2: Automated, Streamlined, and Accurate Absolute Binding Free-Energy Calculations

Haohao Fu, Christophe Chipot, Xueguang Shao, 2021, J. Chem. Inf. Model..

How Do Membrane Transporters Sense pH? The Case of the Mitochondrial ADP–ATP Carrier

C. Chipot, Eva-Maria Krammer, F. Dehez, 2013 .

String method for Protein-Protein Binding Free Energy Calculations.

Wei Jiang, Sunhwan Jo, Donghyuk Suh, 2019, Journal of chemical theory and computation.

NAMD Version 2.9

David M. Kunzman, Eric J. Bohm, James C. Phillips, 2011 .

Peptides at Membrane Surfaces and their Role in Prebiotic Evolution

Michael A. Wilson, A. Pohorille, C. Chipot, 2002 .

Free Energy Methods for the Description of Molecular Processes.

C. Chipot, 2022, Annual review of biophysics.

Affordable Membrane Permeability Calculations: Permeation of Short-Chain Alcohols through Pure-Lipid Bilayers and a Mammalian Cell Membrane.

C. Chipot, J. Comer, Yi Wang, 2019, Journal of chemical theory and computation.

Link between Membrane Composition and Permeability to Drugs.

C. Chipot, J. Comer, Yi Wang, 2018, Journal of chemical theory and computation.

Diffusive Models of Membrane Permeation with Explicit Orientational Freedom.

K. Schulten, C. Chipot, J. Comer, 2014, Journal of chemical theory and computation.

Computational Assessment of Protein-Protein Binding Specificity within a Family of Synaptic Surface Receptors.

C. Chipot, Prithviraj Nandigrami, F. Dehez, 2022, The journal of physical chemistry. B.

An ab initio strategy for handling induction phenomena in metal ion complexes

C. Chipot, F. Dehez, F. Javier Luque, 2008 .

Edge effects control helical wrapping of carbon nanotubes by polysaccharides.

C. Chipot, W. Cai, X. Shao, 2012, Nanoscale.

Mechanism of action of HBV capsid assembly modulators predicted from binding to early assembly intermediates

C. Chipot, R. Schinazi, J. Gumbart, 2020, bioRxiv.

Free-energy cost for translocon-assisted insertion of membrane proteins

Klaus Schulten, Christophe Chipot, James Gumbart, 2011, Proceedings of the National Academy of Sciences.

Induced Night-Vision by Singlet-Oxygen-Mediated Activation of Rhodopsin.

C. Chipot, W. Cai, D. Roca‐Sanjuán, 2019, The journal of physical chemistry letters.

Perturbations of Native Membrane Protein Structure in Alkyl Phosphocholine Detergents: A Critical Assessment of NMR and Biophysical Studies

C. Chipot, P. Schanda, G. Veglia, 2018, Chemical reviews.

Leveraging the Information from Markov State Models To Improve the Convergence of Umbrella Sampling Simulations.

Sunhwan Jo, Donghyuk Suh, Ziwei He, 2016, The journal of physical chemistry. B.

Modulation of membrane permeability by carbon dioxide

Xueguang Shao, François Dehez, Wensheng Cai, 2020, J. Comput. Chem..

Gating of a pH-Sensitive K2P Potassium Channel by an Electrostatic Effect of Basic Sensor Residues on the Selectivity Filter

C. Chipot, F. González-Nilo, M. Niemeyer, 2011, PloS one.

Enhanced configurational sampling with hybrid non-equilibrium molecular dynamics-Monte Carlo propagator.

C. Chipot, B. Roux, B. Radak, 2018, The Journal of chemical physics.

Multiple-Replica Strategies for Free-Energy Calculations in NAMD: Multiple-Walker Adaptive Biasing Force and Walker Selection Rules.

K. Schulten, C. Chipot, J. Comer, 2014, Journal of chemical theory and computation.

Can Absolute Free Energies of Association Be Estimated from Molecular Mechanical Simulations? The Biotin−Streptavidin System Revisited

Christophe Chipot, C. Chipot, Surjit B. Dixit and, 2001 .

Free energy calculations : theory and applications in chemistry and biology

A. Pohorille, C. Chipot, 2007 .

Oligomerization state of photosynthetic core complexes is correlated with the dimerization affinity of a transmembrane helix.

K. Schulten, C. Chipot, A. Senes, 2011, Journal of the American Chemical Society.

Conformational transitions of the serotonin 5-HT3 receptor

C. Chipot, P. Corringer, J. Neyton, 2018, Nature.

Mouse serotonin 5-HT3 receptor, serotonin-bound, I2 conformation

C. Chipot, P. Corringer, J. Neyton, 2018 .

Energetics of ion transport in a peptide nanotube.

Christophe Chipot, François Dehez, Mounir Tarek, 2007, The journal of physical chemistry. B.

Structural and energetic study of cation-π-cation interactions in proteins.

C. Chipot, F. Dehez, C. Curutchet, 2017, Physical chemistry chemical physics : PCCP.

Comprar Free Energy Calculations · Theory and Applications in Chemistry and Biology | Chipot, Christophe | 9783540736172 | Springer

Christophe Chipot, Andrew Pohorille, A. Pohorille, 2007 .

High-speed atomic force microscopy shows that annexin V stabilizes membranes on the second timescale.

Christophe Chipot, Simon Scheuring, C. Chipot, 2016, Nature nanotechnology.

Rational determination of transfer free energies of small drugs across the water-oil interface.

Christophe Chipot, C. Chipot, Delphine Bas, 2002, Journal of medicinal chemistry.

High-chloride concentrations abolish the binding of adenine nucleotides in the mitochondrial ADP/ATP carrier family.

C. Chipot, Eva-Maria Krammer, F. Dehez, 2009, Biophysical journal.

Repurposing Existing Molecular Machines through Accurate Regulation of Cooperative Motions.

C. Chipot, W. Cai, X. Shao, 2020, The journal of physical chemistry letters.

Overcoming Free-Energy Barriers with a Seamless Combination of a Biasing Force and a Collective Variable-Independent Boost Potential.

C. Chipot, W. Cai, X. Shao, 2021, Journal of chemical theory and computation.

A Companion Guide to the String Method with Swarms of Trajectories: Characterization, Performance, and Pitfalls.

C. Chipot, E. Tajkhorshid, W. Cai, 2022, Journal of chemical theory and computation.

Impact of the Unstirred Water Layer on the Permeation of Small-Molecule Drugs

C. Chipot, R. Sun, Christopher Kang, 2024, Journal of Chemical Information and Modeling.

Modeling amino acid side chains. 2. Determination of point charges from electrostatic properties: toward transferable point charge models

Christophe Chipot, Harold A. Scheraga, János G. Ángyán, 1993 .

Modeling amino acid side chains. 1. Determination of net atomic charges from ab initio self-consistent-field molecular electrostatic properties

Christophe Chipot, Harold A. Scheraga, Bernard Maigret, 1992 .