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Molecular Simulation Volume 42, 2016 - Issue 13: Free Energy Simulations
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Articles

Concepts and protocols for electrostatic free energies

Thomas SimonsonLaboratoire de Biochimie (CNRS UMR7654), Ecole Polytechnique, Palaiseau, France.Correspondence[email protected] [email protected]
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Benoît RouxDepartment of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL, USA.;Biosciences Division, Argonne National Laboratory, Argonne, IL, USA.Correspondence[email protected] [email protected]
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Pages 1090-1101 | Received 06 Oct 2015, Accepted 14 Nov 2015, Published online: 05 Jul 2016

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Brandon Walker, Zhifeng Jing & Pengyu Ren. (2021) Molecular dynamics free energy simulations of ATP:Mg2+ and ADP:Mg2+ using the polarisable force field AMOEBA. Molecular Simulation 47:5, pages 439-448.
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Moses K. J. Chung, Ryan J. Miller, Borna Novak, Zhi Wang & Jay W. Ponder. (2023) Accurate Host–Guest Binding Free Energies Using the AMOEBA Polarizable Force Field. Journal of Chemical Information and Modeling 63:9, pages 2769-2782.
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Julie Puyo-Fourtine, Marie Juillé, Jérôme Hénin, Carine Clavaguéra & Elise Duboué-Dijon. (2022) Consistent Picture of Phosphate–Divalent Cation Binding from Models with Implicit and Explicit Electronic Polarization. The Journal of Physical Chemistry B 126:22, pages 4022-4034.
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Zhiyi Wu & Philip C. Biggin. (2022) Correction Schemes for Absolute Binding Free Energies Involving Lipid Bilayers. Journal of Chemical Theory and Computation 18:4, pages 2657-2672.
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E. Duboué-Dijon & J. Hénin. (2021) Building intuition for binding free energy calculations: Bound state definition, restraints, and symmetry. The Journal of Chemical Physics 154:20.
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Thomas T. Joseph, Weiming Bu, Wenzhen Lin, Lioudmila Zoubak, Alexei Yeliseev, Renyu Liu, Roderic G. Eckenhoff & Grace Brannigan. (2021) Ketamine Metabolite (2 R ,6 R )-Hydroxynorketamine Interacts with μ and κ Opioid Receptors . ACS Chemical Neuroscience 12:9, pages 1487-1497.
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Martin Amezcua, Léa El Khoury & David L. Mobley. (2021) SAMPL7 Host–Guest Challenge Overview: assessing the reliability of polarizable and non-polarizable methods for binding free energy calculations. Journal of Computer-Aided Molecular Design 35:1, pages 1-35.
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Yuanjun Shi, Marie L. Laury, Zhi Wang & Jay W. Ponder. (2020) AMOEBA binding free energies for the SAMPL7 TrimerTrip host–guest challenge. Journal of Computer-Aided Molecular Design 35:1, pages 79-93.
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Denilson Mendes de Oliveira, Samual R. Zukowski, Vladimir Palivec, Jérôme Hénin, Hector Martinez-Seara, Dor Ben-Amotz, Pavel Jungwirth & Elise Duboué-Dijon. (2020) Binding of divalent cations to acetate: molecular simulations guided by Raman spectroscopy. Physical Chemistry Chemical Physics 22:41, pages 24014-24027.
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E. Duboué-Dijon, M. Javanainen, P. Delcroix, P. Jungwirth & H. Martinez-Seara. (2020) A practical guide to biologically relevant molecular simulations with charge scaling for electronic polarization. The Journal of Chemical Physics 153:5.
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Zhifeng Jing, Rui Qi, Marc Thibonnier & Pengyu Ren. (2019) Molecular Dynamics Study of the Hybridization between RNA and Modified Oligonucleotides. Journal of Chemical Theory and Computation 15:11, pages 6422-6432.
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Rui Qi, Brandon Walker, Zhifeng Jing, Maiya Yu, Gabriel Stancu, Ramakrishna Edupuganti, Kevin N. Dalby & Pengyu Ren. (2019) Computational and Experimental Studies of Inhibitor Design for Aldolase A. The Journal of Physical Chemistry B 123:28, pages 6034-6041.
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Zachary C. Holden, Bhaskar Rana & John M. Herbert. (2019) Analytic gradient for the QM/MM-Ewald method using charges derived from the electrostatic potential: Theory, implementation, and application to ab initio molecular dynamics simulation of the aqueous electron . The Journal of Chemical Physics 150:14.
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Shu-Ching Ou & B. Montgomery Pettitt. (2019) Free Energy Calculations Based on Coupling Proximal Distribution Functions and Thermodynamic Cycles. Journal of Chemical Theory and Computation 15:4, pages 2649-2658.
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Toru Ekimoto, Tsutomu Yamane & Mitsunori Ikeguchi. (2018) Elimination of Finite-Size Effects on Binding Free Energies via the Warp-Drive Method. Journal of Chemical Theory and Computation 14:12, pages 6544-6559.
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Francesco Villa, Alexander D. MacKerellJr.Jr., Benoît Roux & Thomas Simonson. (2018) Classical Drude Polarizable Force Field Model for Methyl Phosphate and Its Interactions with Mg 2+ . The Journal of Physical Chemistry A 122:29, pages 6147-6155.
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Michael Bielecki, Graeme W. Howe & Ronald Kluger. (2018) Charge Dispersion and Its Effects on the Reactivity of Thiamin-Derived Breslow Intermediates. Biochemistry 57:26, pages 3867-3872.
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Manjeet Kumar, Thomas Simonson, Gilles Ohanessian & Carine Clavaguéra. (2018) Corrigendum: Structure and Thermodynamics of Mg:Phosphate Interactions in Water: A Simulation Study. ChemPhysChem 19:9, pages 1117-1117.
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Nicolas Panel, Francesco Villa, Ernesto J. Fuentes & Thomas Simonson. (2018) Accurate PDZ/Peptide Binding Specificity with Additive and Polarizable Free Energy Simulations. Biophysical Journal 114:5, pages 1091-1102.
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Martin A. Olsson, Alfonso T. García-Sosa & Ulf Ryde. (2017) Binding affinities of the farnesoid X receptor in the D3R Grand Challenge 2 estimated by free-energy perturbation and docking. Journal of Computer-Aided Molecular Design 32:1, pages 211-224.
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Timothy T. Duignan, Marcel D. Baer, Gregory K. Schenter & Chistopher J. Mundy. (2017) Electrostatic solvation free energies of charged hard spheres using molecular dynamics with density functional theory interactions. The Journal of Chemical Physics 147:16.
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Nicolas Panel, Young Joo Sun, Ernesto J. Fuentes & Thomas Simonson. (2017) A Simple PB/LIE Free Energy Function Accurately Predicts the Peptide Binding Specificity of the Tiam1 PDZ Domain. Frontiers in Molecular Biosciences 4.
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David L. MobleyMichael K. Gilson. (2017) Predicting Binding Free Energies: Frontiers and Benchmarks. Annual Review of Biophysics 46:1, pages 531-558.
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Shu-Ching Ou, Justin A. Drake & B. Montgomery Pettitt. (2017) Nonpolar Solvation Free Energy from Proximal Distribution Functions. The Journal of Physical Chemistry B 121:15, pages 3555-3564.
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Thomas Simonson, Gerhard Hummer & Benoît Roux. (2017) Equivalence of M- and P-Summation in Calculations of Ionic Solvation Free Energies. The Journal of Physical Chemistry A 121:7, pages 1525-1530.
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Jiewei Hong, Robert J. Hamers, Joel A. Pedersen & Qiang Cui. (2017) A Hybrid Molecular Dynamics/Multiconformer Continuum Electrostatics (MD/MCCE) Approach for the Determination of Surface Charge of Nanomaterials. The Journal of Physical Chemistry C 121:6, pages 3584-3596.
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Yuqing Zheng & Qiang Cui. (2016) Microscopic mechanisms that govern the titration response and p K a values of buried residues in staphylococcal nuclease mutants . Proteins: Structure, Function, and Bioinformatics 85:2, pages 268-281.
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