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Calibration of the dianionic phosphate group: Validation on the recognition site of the homodimeric enzyme phosphoglucose isomerase
Marion Devillers, Jean‐Philip Piquemal, Laurent Salmon and Nohad Gresh Journal of Computational Chemistry 41(8) 839 (2020) https://doi.org/10.1002/jcc.26134
Perspective: Ab initio force field methods derived from quantum mechanics
Peng Xu, Emilie B. Guidez, Colleen Bertoni and Mark S. Gordon The Journal of Chemical Physics 148(9) (2018) https://doi.org/10.1063/1.5009551
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
Calibration of 1,2,4-Triazole-3-Thione, an Original Zn-Binding Group of Metallo-β-Lactamase Inhibitors. Validation of a Polarizable MM/MD Potential by Quantum Chemistry
Complexes of a Zn‐metalloenzyme binding site with hydroxamate‐containing ligands. A case for detailed benchmarkings of polarizable molecular mechanics/dynamics potentials when the experimental binding structure is unknown
Nohad Gresh, David Perahia, Benoit de Courcy, Johanna Foret, Céline Roux, Lea El‐Khoury, Jean‐Philip Piquemal and Laurent Salmon Journal of Computational Chemistry 37(32) 2770 (2016) https://doi.org/10.1002/jcc.24503
Quantum Modeling of Complex Molecular Systems
Nohad Gresh, Krystel El Hage, Elodie Goldwaser, et al. Challenges and Advances in Computational Chemistry and Physics, Quantum Modeling of Complex Molecular Systems 21 1 (2015) https://doi.org/10.1007/978-3-319-21626-3_1
Stacked and H-Bonded Cytosine Dimers. Analysis of the Intermolecular Interaction Energies by Parallel Quantum Chemistry and Polarizable Molecular Mechanics.
Substituent-Modulated Affinities of Halobenzene Derivatives to the HIV-1 Integrase Recognition Site. Analyses of the Interaction Energies by Parallel Quantum Chemical and Polarizable Molecular Mechanics
Krystel El Hage, Jean-Philip Piquemal, Zeina Hobaika, Richard G. Maroun and Nohad Gresh The Journal of Physical Chemistry A 118(41) 9772 (2014) https://doi.org/10.1021/jp5079899
Fragmentation Methods: A Route to Accurate Calculations on Large Systems
Mark S. Gordon, Dmitri G. Fedorov, Spencer R. Pruitt and Lyudmila V. Slipchenko Chemical Reviews 112(1) 632 (2012) https://doi.org/10.1021/cr200093j
Multi-scale Quantum Models for Biocatalysis
G.A. Cisneros, T.A. Darden, N. Gresh, et al. Challenges and Advances in Computational Chemistry and Physics, Multi-scale Quantum Models for Biocatalysis 7 137 (2009) https://doi.org/10.1007/978-1-4020-9956-4_6
Energy Analysis of Zn Polycoordination in a Metalloprotein Environment and of the Role of a Neighboring Aromatic Residue. What Is the Impact of Polarization?
Benoit de Courcy, Jean-Philip Piquemal and Nohad Gresh Journal of Chemical Theory and Computation 4(10) 1659 (2008) https://doi.org/10.1021/ct800200j
Anisotropic, Polarizable Molecular Mechanics Studies of Inter- and Intramolecular Interactions and Ligand−Macromolecule Complexes. A Bottom-Up Strategy
Nohad Gresh, G. Andrés Cisneros, Thomas A. Darden and Jean-Philip Piquemal Journal of Chemical Theory and Computation 3(6) 1960 (2007) https://doi.org/10.1021/ct700134r
Modeling of Copper(II) Complexes with the SIBFA Polarizable Molecular Mechanics Procedure. Application to a New Class of HIV-1 Protease Inhibitors
Marie Ledecq, Florence Lebon, François Durant, et al. The Journal of Physical Chemistry B 107(38) 10640 (2003) https://doi.org/10.1021/jp0354604
Inclusion of the ligand field contribution in a polarizable molecular mechanics: SIBFA‐LF
Jean‐Philip Piquemal, Ben Williams‐Hubbard, Natalie Fey, Robert J. Deeth, Nohad Gresh and Claude Giessner‐Prettre Journal of Computational Chemistry 24(16) 1963 (2003) https://doi.org/10.1002/jcc.10354
Modeling Copper(I) Complexes: SIBFA Molecular Mechanics versus ab Initio Energetics and Geometrical Arrangements
N. Gresh, C. Policar and C. Giessner-Prettre The Journal of Physical Chemistry A 106(23) 5660 (2002) https://doi.org/10.1021/jp0106146
Binding of D‐ and L‐captopril inhibitors to metallo‐β‐lactamase studied by polarizable molecular mechanics and quantum mechanics
Jens Antony, Nohad Gresh, Lars Olsen, Lars Hemmingsen, Christopher J. Schofield and Rogert Bauer Journal of Computational Chemistry 23(13) 1281 (2002) https://doi.org/10.1002/jcc.10111
Parallelab initio and molecular mechanics investigation of polycoordinated Zn(II) complexes with model hard and soft ligands: Variations of binding energy and of its components with number and charges of ligands
Many-Body Effects in Systems of Peptide Hydrogen-Bonded Networks and Their Contributions to Ligand Binding: A Comparison of the Performances of DFT and Polarizable Molecular Mechanics
Hong Guo, Nohad Gresh, Bernard P. Roques and Dennis R. Salahub The Journal of Physical Chemistry B 104(41) 9746 (2000) https://doi.org/10.1021/jp0012247
Modeling of some structural and vibrational properties of CO : CO2 complexes in gas phase and embedded in solid argon
Critical Role of Anisotropy for the Dimerization Energies of Two Protein−Protein Recognition Motifs: cis-N-Methylacetamide versus a β-Sheet Conformer of Alanine Dipeptide. A Joint ab Initio, Density Functional Theory, and Molecular Mechanics Investigation
Nohad Gresh, Hong Guo, Dennis R. Salahub, Bernard P. Roques and Sherif A. Kafafi Journal of the American Chemical Society 121(34) 7885 (1999) https://doi.org/10.1021/ja9742489
Conformational properties of a model alanyl dipeptide and of alanine-derived oligopeptides: Effects of solvation in water and in organic solvents—A combined SIBFA/continuum reaction field, ab initio self-consistent field, and density functional theory investigation
Model, Multiply Hydrogen-Bonded Water Oligomers (N = 3−20). How Closely Can a Separable, ab Initio-Grounded Molecular Mechanics Procedure Reproduce the Results of Supermolecule Quantum Chemical Computations?
Thermolysin-inhibitor binding: Effect of the His231 → Ala mutation on the relative affinities of thiolate versus phosphoramidate inhibitors—a model theoretical investigation incorporating acontinuum reaction field hydration model
Comparative binding energetics of Mg2+, Ca2+, Zn2+, and Cd2+ to biologically relevant ligands: Combined ab initio SCF supermolecule and molecular mechanics investigation
Energetics of Zn2+ binding to a series of biologically relevant ligands: A molecular mechanics investigation grounded on ab initio self‐consistent field supermolecular computations