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Development, validation, and applications of anisotropic polarizable molecular mechanics to study ligand and drug-receptor interactions

Current pharmaceutical design, 2006-06, Vol.12 (17), p.2121

Gresh, Nohad

2006

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Towards a force field based on density fitting

The Journal of chemical physics, 2006-03, Vol.124 (10), p.104101-104101-12

2006

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Many-body exchange-repulsion in polarizable molecular mechanics. I. orbital-based approximations and applications to hydrated metal cation complexes

Journal of computational chemistry, 2011-11, Vol.32 (14), p.2949-2957

2011

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Multimolecular complexes of the phosphodiester anion with Zn(II) or Mg(II) and water molecules—Preliminary validations of a polarizable potential by ab initio quantum chemistry

Journal of computational chemistry, 2021-07, Vol.42 (20), p.1430-1446

2021

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4-( N -Alkyl- and -Acyl-amino)-1,2,4-triazole-3-thione Analogs as Metallo-β-Lactamase Inhibitors: Impact of 4-Linker on Potency and Spectrum of Inhibition

Biomolecules (Basel, Switzerland), 2020-07, Vol.10 (8), p.1094

2020

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Quantum-Chemistry Based Design of Halobenzene Derivatives With Augmented Affinities for the HIV-1 Viral G4/C16 Base-Pair

Frontiers in chemistry, 2020-06, Vol.8, p.440-440

2020

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Spectrometric and computational studies of the binding of HIV-1 integrase inhibitors to viral DNA extremities

PeerJ physical chemistry, 2019-12, Vol.1, p.e6

2019

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A Simple Isomerization of the Purine Scaffold of a Kinase Inhibitor, Roscovitine, Affords a Four- to Seven-Fold Enhancement of Its Affinity for Four CDKs. Could This Be Traced Back to Conjugation-Induced Stiffenings/Loosenings of Rotational Barriers?

ACS omega, 2017-07, Vol.2 (7), p.3467-3474

2017

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Rational Design, Synthesis, and DNA Binding Properties of Novel Sequence-Selective Peptidyl Congeners of Ametantrone

ChemMedChem, 2010-07, Vol.5 (7), p.1080-1091

2010

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Assessment of SAPT and Supermolecular EDA Approaches for the Development of Separable and Polarizable Force Fields

Journal of chemical theory and computation, 2021-05, Vol.17 (5), p.2759-2774

2021

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Study of the inhibition mechanism of HIV-1 integrase by diketoacids molecules

Journal of Virus Eradication, 2016-05, Vol.2, p.14-14

2016

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Tinker-HP: a massively parallel molecular dynamics package for multiscale simulations of large complex systems with advanced point dipole polarizable force fields

Chemical science (Cambridge), 2018, Vol.9 (4), p.956-972

2018

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Anisotropic, Polarizable Molecular Mechanics Studies of Inter- and Intramolecular Interactions and Ligand−Macromolecule Complexes. A Bottom-Up Strategy

Journal of chemical theory and computation, 2007-11, Vol.3 (6), p.1960-1986

2007

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Assessment of SAPT and Supermolecular EDAs Approaches for the Development of Separable and Polarizable force fields

Journal of chemical theory and computation, 2021-04, Vol.17 (5)

2021

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General Model for Treating Short-Range Electrostatic Penetration in a Molecular Mechanics Force Field

Journal of chemical theory and computation, 2015-06, Vol.11 (6), p.2609-2618

2015

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

Journal of chemical theory and computation, 2022-06, Vol.18 (6), p.3607-3621

2022

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Toward a Separate Reproduction of the Contributions to the Hartree−Fock and DFT Intermolecular Interaction Energies by Polarizable Molecular Mechanics with the SIBFA Potential

Journal of chemical theory and computation, 2007-05, Vol.3 (3), p.824-837

2007

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

Journal of computational chemistry, 2020-03, Vol.41 (8), p.839-854

2020

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

Journal of chemical information and modeling, 2022-12, Vol.62 (24), p.6649-6666

2022

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A supervised fitting approach to force field parametrization with application to the SIBFA polarizable force field

Journal of computational chemistry, 2014-08, Vol.35 (21), p.1577-1591

2014

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Interfacial Water Many-Body Effects Drive Structural Dynamics and Allosteric Interactions in SARS-CoV‑2 Main Protease Dimerization Interface

The journal of physical chemistry letters, 2021-07, Vol.12 (26), p.6218-6226

2021

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Design and synthesis of a peptide derivative of ametantrone targeting the major groove of the d(GGCGCC) 2 palindromic sequence

New journal of chemistry, 2020-03, Vol.44 (9), p.3624-3631

2020

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Channeling through Two Stacked Guanine Quartets of One and Two Alkali Cations in the Li+, Na+, K+, and Rb+ Series. Assessment of the Accuracy of the SIBFA Anisotropic Polarizable Molecular Mechanics Potential

The journal of physical chemistry. B, 2017-04, Vol.121 (16), p.3997-4014

2017

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Design and synthesis of a peptide derivative of ametantrone targeting the major groove of the d(GGCGCC) palindromic sequence

New journal of chemistry, 2020-03, Vol.44 (9), p.3624-3631

2020

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Enforcing Local DNA Kinks by Sequence‐Selective Trisintercalating Oligopeptides of a Tricationic Porphyrin: A Polarizable Molecular Dynamics Study

Chemphyschem, 2024-02, Vol.25 (3), p.e202300776-n/a

2024

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Development, validation, and applications of anisotropic polarizable molecular mechanics to study ligand and drug-receptor interactions

Towards a force field based on density fitting

Many-body exchange-repulsion in polarizable molecular mechanics. I. orbital-based approximations and applications to hydrated metal cation complexes

Multimolecular complexes of the phosphodiester anion with Zn(II) or Mg(II) and water molecules—Preliminary validations of a polarizable potential by ab initio quantum chemistry

4-( N -Alkyl- and -Acyl-amino)-1,2,4-triazole-3-thione Analogs as Metallo-β-Lactamase Inhibitors: Impact of 4-Linker on Potency and Spectrum of Inhibition

Quantum-Chemistry Based Design of Halobenzene Derivatives With Augmented Affinities for the HIV-1 Viral G4/C16 Base-Pair

Spectrometric and computational studies of the binding of HIV-1 integrase inhibitors to viral DNA extremities

A Simple Isomerization of the Purine Scaffold of a Kinase Inhibitor, Roscovitine, Affords a Four- to Seven-Fold Enhancement of Its Affinity for Four CDKs. Could This Be Traced Back to Conjugation-Induced Stiffenings/Loosenings of Rotational Barriers?

Rational Design, Synthesis, and DNA Binding Properties of Novel Sequence-Selective Peptidyl Congeners of Ametantrone

Assessment of SAPT and Supermolecular EDA Approaches for the Development of Separable and Polarizable Force Fields

Study of the inhibition mechanism of HIV-1 integrase by diketoacids molecules

Tinker-HP: a massively parallel molecular dynamics package for multiscale simulations of large complex systems with advanced point dipole polarizable force fields

Anisotropic, Polarizable Molecular Mechanics Studies of Inter- and Intramolecular Interactions and Ligand−Macromolecule Complexes. A Bottom-Up Strategy

Assessment of SAPT and Supermolecular EDAs Approaches for the Development of Separable and Polarizable force fields

General Model for Treating Short-Range Electrostatic Penetration in a Molecular Mechanics Force Field

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

Toward a Separate Reproduction of the Contributions to the Hartree−Fock and DFT Intermolecular Interaction Energies by Polarizable Molecular Mechanics with the SIBFA Potential

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

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

A supervised fitting approach to force field parametrization with application to the SIBFA polarizable force field

Interfacial Water Many-Body Effects Drive Structural Dynamics and Allosteric Interactions in SARS-CoV‑2 Main Protease Dimerization Interface

Design and synthesis of a peptide derivative of ametantrone targeting the major groove of the d(GGCGCC) 2 palindromic sequence

Channeling through Two Stacked Guanine Quartets of One and Two Alkali Cations in the Li+, Na+, K+, and Rb+ Series. Assessment of the Accuracy of the SIBFA Anisotropic Polarizable Molecular Mechanics Potential

Design and synthesis of a peptide derivative of ametantrone targeting the major groove of the d(GGCGCC) palindromic sequence

Enforcing Local DNA Kinks by Sequence‐Selective Trisintercalating Oligopeptides of a Tricationic Porphyrin: A Polarizable Molecular Dynamics Study

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