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Modeling Structural Coordination and Ligand Binding in Zinc Proteins with a Polarizable Potential
Jiajing Zhang
,
Wei Yang
,
Jean-Philip Piquemal
,
Pengyu Ren
Journal articles
hal-02126837v1
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Implicit Solvents for the Polarizable Atomic Multipole AMOEBA Force Field
Rae Corrigan
,
Guowei Qi
,
Andrew Thiel
,
Jack Lynn
,
Brandon D Walker
et al.
Journal articles
hal-03183306v1
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Implementation of Geometry Dependent Charge Flux into Polarizable AMOEBA+ Potential
Chengwen Liu
,
Jean-Philip Piquemal
,
Pengyu Ren
Journal articles
hal-02410854v1
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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 articles
hal-03220156v1
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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 articles
hal-03624156v1
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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 articles
hal-03624169v1
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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 articles
hal-02377726v1
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On the Quantum Chemical Nature of Lead(II) "Lone Pair
Christophe Gourlaouen
,
Jean-Philip Piquemal
Journal articles
hal-03232340v1
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Capturing Many-Body Interactions with Classical Dipole Induction Models
Chengwen Liu
,
Rui R. Qi
,
Qiantao Qi
,
J.-P. Piquemal
,
Pengyu Ren
et al.
Journal articles
hal-02126842v1
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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
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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 articles
hal-03508892v1
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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 articles
hal-02126833v1
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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 articles
hal-02126853v1
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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
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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.
Journal articles
hal-01405847v1
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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.
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.
Journal articles
hal-02921299v1
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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 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.
Journal articles
hal-01821899v1
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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
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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.
Journal articles
hal-02377718v1
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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 articles
hal-02126799v1
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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 articles
hal-02299827v1
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AMOEBA Polarizable Atomic Multipole Force Field for Nucleic Acids
Changsheng Zhang
,
Chao Lu
,
Zhifeng F Jing
,
Chuanjie Wu
,
Jean-Philip Piquemal
et al.
Journal articles
hal-02126772v1
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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 articles
hal-02126806v1
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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 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 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 articles
hal-03179730v1
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Accurate biomolecular simulations account for electronic polarization
Josef Melcr
,
Jean-Philip Piquemal
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.
Journal articles
hal-02943694v1
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