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Structure: Internal structure identifier : 454935

Modeling Structural Coordination and Ligand Binding in Zinc Proteins with a Polarizable Potential

Jiajing Zhang , Wei Yang , Jean-Philip Piquemal , Pengyu Ren
Journal of Chemical Theory and Computation, 2012, 8 (4), pp.1314-1324. ⟨10.1021/ct200812y⟩
Journal articles hal-02126837v1

Implicit Solvents for the Polarizable Atomic Multipole AMOEBA Force Field

Rae Corrigan , Guowei Qi , Andrew Thiel , Jack Lynn , Brandon D Walker et al.
Journal of Chemical Theory and Computation, 2021, ⟨10.1021/acs.jctc.0c01286⟩
Journal articles hal-03183306v1

Implementation of Geometry Dependent Charge Flux into Polarizable AMOEBA+ Potential

Chengwen Liu , Jean-Philip Piquemal , Pengyu Ren
Journal of Physical Chemistry Letters, 2020, 11 (2), pp.419-426. ⟨10.1021/acs.jpclett.9b03489⟩
Journal articles hal-02410854v1

Interfacial Water Many-body Effects Drive Structural Dynamics and Allosteric interactions in SARS-CoV-2 Main Protease Dimerization Interface

Dina El Ahdab , Louis Lagardère , Theo Jaffrelot Inizan , Frédéric Célerse , Chengwen Liu et al.
Journal of Physical Chemistry Letters, 2021, 12, pp.6218-6226. ⟨10.1021/acs.jpclett.1c01460⟩
Journal articles hal-03220156v1

Accurate Deep Learning-aided Density-free Strategy for Many-Body Dispersion-corrected Density Functional Theory

Pier Paolo Poier , Théo Jaffrelot Inizan , Olivier Adjoua , Louis Lagardère , Jean-Philip Piquemal et al.
Journal of Physical Chemistry Letters, 2022, 13 (19), pp.4381-4388. ⟨10.1021/acs.jpclett.2c00936⟩
Journal articles hal-03624156v1

Targeting the Major Groove of the Palindromic d(GGCGCC)2 Sequence by Oligopeptide Derivatives of Anthraquinone Intercalators

Krystel El Hage , Giovanni Ribaudo , Louis Lagardère , Alberto Ongaro , Philippe H. Kahn et al.
Journal of Chemical Information and Modeling, 2022, ⟨10.1021/acs.jcim.2c00337⟩
Journal articles hal-03624169v1

Calibration of the dianionic phosphate group. Validation on the recognition site of the homodimeric enzyme phosphoglucose isomerase.

M. Devillers , Jean-Philip Piquemal , L. Salmon , N. Gresh
Journal of Computational Chemistry, 2020, 41 (8), pp.839-854. ⟨10.1002/jcc.26134⟩
Journal articles hal-02377726v1

On the Quantum Chemical Nature of Lead(II) "Lone Pair

Christophe Gourlaouen , Jean-Philip Piquemal
Molecules, 2022, 27 (1), pp.27. ⟨10.3390/molecules27010027⟩
Journal articles hal-03232340v1

Capturing Many-Body Interactions with Classical Dipole Induction Models

Chengwen Liu , Rui R. Qi , Qiantao Qi , J.-P. Piquemal , Pengyu Ren et al.
Journal of Chemical Theory and Computation, 2017, 13 (6), pp.2751-2761. ⟨10.1021/acs.jctc.7b00225⟩
Journal articles hal-02126842v1

β-actin plasticity is modulated by coordinated actions of histidine 73 methylation, nucleotide type, and ions

Adrien Schahl , Louis Lagardère , Brandon Walker , Pengyu Ren , Antoine Jégoud et al.
2022
Preprints, Working Papers, ... hal-03904639v1

Development of the Quantum Inspired SIBFA Many-Body Polarizable Force Field: Enabling Condensed Phase Molecular Dynamics Simulations.

S. Naseem Kahn , L. Lagardère , C. Narth , G. A. Cisneros , P. Ren et al.
Journal of Chemical Theory and Computation, 2022, 18 (6), pp.3607-3621. ⟨10.1021/acs.jctc.2c00029⟩
Journal articles hal-03508892v1

Polarizable Molecular Dynamics Simulation of Zn(II) in Water Using the AMOEBA Force Field

Johnny Wu , Jean-Philip Piquemal , Robin Chaudret , Peter Reinhardt , Pengyu Ren et al.
Journal of Chemical Theory and Computation, 2010, 6 (7), pp.2059-2070. ⟨10.1021/ct100091j⟩
Journal articles hal-02126833v1

Elucidating the Phosphate Binding Mode of Phosphate-Binding Protein: The Critical Effect of Buffer Solution

Rui R. Qi , Zhifeng F Jing , Chengwen Liu , Jean-Philip Piquemal , Kevin Dalby et al.
Journal of Physical Chemistry B, 2018, 122 (24), pp.6371-6376. ⟨10.1021/acs.jpcb.8b03194⟩
Journal articles hal-02126853v1

Generalized Many-Body Dispersion Correction through Random-phase Approximation for Chemically Accurate Density Functional Theory

Pier Paolo Poier , Olivier Adjoua , Louis Lagardère , Jean-Philip Piquemal
2022
Preprints, Working Papers, ... hal-03819436v1

An Optimized Charge Penetration Model for Use with the AMOEBA Force Field

Joshua A. Rackers , Qiantao Wang , Chengwen Liu , Jean-Philip Piquemal , Pengyu Ren et al.
Physical Chemistry Chemical Physics, 2016, ⟨10.1039/C6CP06017J⟩
Journal articles hal-01405847v1

Computationally driven discovery of targeting SARS-CoV-2 Mpro inhibitors: from design to experimental validation

Léa El Khoury , Zhifeng Jing , Daniele Loco , Alberto Cuzzolin , Alessandro Deplano et al.
Chemical Science, 2022, ⟨10.1039/D1SC05892D⟩
Journal articles hal-03361062v1
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NCIPLOT and the analysis of noncovalent interactions using the reduced density gradient

Rubén Laplaza , Francesca Peccati , Roberto A. Boto , Chaoyu Quan , Alessandra Carbone et al.
WIREs Computational Molecular Science, 2021, 11 (2), pp.e1497. ⟨10.1002/wcms.1497⟩
Journal articles hal-02921299v1

Correction to “Massively Parallel Implementation of Steered Molecular Dynamics in Tinker-HP: Comparisons of Polarizable and Nonpolarizable Simulations of Realistic Systems”

Frédéric Célerse , Louis Lagardère , Etienne Derat , Jean-Philip Piquemal
Journal of Chemical Theory and Computation, 2021, 17 (5), pp.3235-3236. ⟨10.1021/acs.jctc.1c00405⟩
Journal articles hal-03210774v1
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Polarizable force fields for biomolecular simulations: Recent advances and applications

Zhifeng F Jing , Chengwen Liu , Sara y Cheng , Rui Qi , Brandon D Walker et al.
Annual Reviews of Biophysics, 2019, 48, pp.371-394. ⟨10.1146/annurev-biophys-070317-033349⟩
Journal articles hal-01821899v1

Unraveling interactions in large complex systems using quantum chemistry interpretative techniques and new generation polarizable force fields

R. Chaudret , B. de Courcy , A. Marjolin , M.-C. van Severen , P. Ren et al.
INTERNATIONAL CONFERENCE OF COMPUTATIONAL METHODS IN SCIENCES AND ENGINEERING 2009: (ICCMSE 2009), 2009, Rhodes, Greece. pp.699-702
Conference papers hal-02126865v1

Quantum-Chemistry based design of halobenzene derivatives with augmented affinities for the HIV-1 viral G4/C16 base-pair.

Perla El Darazi , Léa El Khoury , Krystel El Hage , Richard G. Maroun , Zeina Hobaika et al.
Frontiers in Chemistry, 2020, 8, pp.440. ⟨10.3389/fchem.2020.00440⟩
Journal articles hal-02377718v1

Modeling Organochlorine Compounds and the σ-Hole Effect Using a Polarizable Multipole Force Field

Xiaojiao Mu , Qiantao Wang , Lee-Ping Wang , Stephen Fried , Jean-Philip Piquemal et al.
Journal of Physical Chemistry B, 2014, 118 (24), pp.6456-6465. ⟨10.1021/jp411671a⟩
Journal articles hal-02126799v1

Molecular Dynamics using Non-variational Polarizable Force Fields: Theory, Periodic Boundary Conditions Implementation and Application to the Bond Capacity Model

Poier Pier Paolo , Louis Lagardère , Jean-Philip Piquemal , Frank Jensen
Journal of Chemical Theory and Computation, 2019, ⟨10.1021/acs.jctc.9b00721⟩
Journal articles hal-02299827v1

AMOEBA Polarizable Atomic Multipole Force Field for Nucleic Acids

Changsheng Zhang , Chao Lu , Zhifeng F Jing , Chuanjie Wu , Jean-Philip Piquemal et al.
Journal of Chemical Theory and Computation, 2018, 14 (4), pp.2084-2108. ⟨10.1021/acs.jctc.7b01169⟩
Journal articles hal-02126772v1

Towards accurate solvation dynamics of divalent cations in water using the polarizable amoeba force field: From energetics to structure

Jean-Philip Piquemal , Lalith Perera , G. Andrés Cisneros , Pengyu Ren , Lee Pedersen et al.
Journal of Chemical Physics, 2006, 125 (5), pp.054511. ⟨10.1063/1.2234774⟩
Journal articles hal-02126806v1

Improvement of the Gaussian Electrostatic Model by Separate Fitting of Coulomb and Exchange-Repulsion Densities and Implementation of a new Dispersion term

Sehr Naseem-Khan , Jean-Philip Piquemal , G. Andrés Cisneros
Journal of Chemical Physics, 2021, ⟨10.1063/5.0072380⟩
Journal articles hal-03353343v1
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Truncated Conjugate Gradient (TCG): an optimal strategy for the analytical evaluation of the many-body polarization energy and forces in molecular simulations

Félix Aviat , Antoine Levitt , Benjamin Stamm , Yvon Maday , Pengyu Ren et al.
Journal of Chemical Theory and Computation, 2017, 13 (1), pp.180-190. ⟨10.1021/acs.jctc.6b00981⟩
Journal articles hal-01395833v4
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Tinker-HP: Accelerating Molecular Dynamics Simulations of Large Complex Systems with Advanced Point Dipole Polarizable Force Fields Using GPUs and Multi-GPU Systems

Olivier Adjoua , Louis Lagardère , Luc-Henri Jolly , Arnaud Durocher , Thibaut Véry et al.
Journal of Chemical Theory and Computation, 2021, 17 (4), pp.2034-2053. ⟨10.1021/acs.jctc.0c01164⟩
Journal articles hal-03179730v1
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Accurate biomolecular simulations account for electronic polarization

Josef Melcr , Jean-Philip Piquemal
Frontiers in Molecular Biosciences, 2019, 6, pp.143. ⟨10.3389/fmolb.2019.00143⟩
Journal articles hal-02283625v1
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High-Resolution Mining of SARS-CoV-2 Main Protease Conformational Space: Supercomputer-Driven Unsupervised Adaptive Sampling

Théo Jaffrelot Inizan , Frederic Célerse , Olivier Adjoua , Dina El Ahdab , Luc-Henri Jolly et al.
Chemical Science, 2021, 12 (13), pp.4889-4907. ⟨10.1039/D1SC00145K⟩
Journal articles hal-02943694v1