ArticleThe journal of physical chemistry letters2017
Extending the Nonbonded Cationic Dummy Model to Account for Ion-Induced Dipole Interactions.
Article in The journal of physical chemistry letters, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 18 papers.
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Who cites it
18 citing papers in PubMed.
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- Engineering Charge Transport by Tunneling in Supramolecular Assemblies through Precise Control of Metal-Ligand Interactions.Small (Weinheim an der Bergstrasse, Germany) · 2025Article
- Development and Application of FeACS omega · 2025Article
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- Allosteric rescue of catalytically impaired ATP phosphoribosyltransferase variants links protein dynamics to active-site electrostatic preorganisation.Nature communications · 2022Article
- Bacterial H-NS contacts DNA at the same irregularly spaced sites in both bridged and hemi-sequestered linear filaments.iScience · 2022Article
- Chelator-Based Parameterization of the 12-6-4 Lennard-Jones Molecular Mechanics Potential for More Realistic Metal Ion-Protein Interactions.Journal of chemical theory and computation · 2022Article
- Rational Engineering of CRISPR-Cas9 Nuclease to Attenuate Position-Dependent Off-Target Effects.The CRISPR journal · 2022Article
- Analysis of Kojic Acid Derivatives as Competitive Inhibitors of Tyrosinase: A Molecular Modeling Approach.Molecules (Basel, Switzerland) · 2021Article
- Parametrization of Trivalent and Tetravalent Metal Ions for the OPC3, OPC, TIP3P-FB, and TIP4P-FB Water Models.Journal of chemical theory and computation · 2021Article
- Coarse-Grained Modeling and Molecular Dynamics Simulations of CaFrontiers in molecular biosciences · 2021Article
- Active-Site Models ofFrontiers in molecular biosciences · 2021Article
- Expanding the Structural Diversity of DNA Methyltransferase Inhibitors.Pharmaceuticals (Basel, Switzerland) · 2020Article
- Systematic Parametrization of Divalent Metal Ions for the OPC3, OPC, TIP3P-FB, and TIP4P-FB Water Models.Journal of chemical theory and computation · 2020Article
- A positive, growth-based PAM screen identifies noncanonical motifs recognized by theScience advances · 2020Article
- Structural and functional insights into theeLife · 2019Article
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4 authors.
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Abstract
Modeling metalloproteins often requires classical molecular dynamics (MD) simulations in order to capture their relevant motions, which in turn necessitates reliable descriptions of the metal centers involved. One of the most successful approaches to date is provided by the "cationic dummy model", where the positive charge of the metal ion is transferred toward dummy particles that are bonded to the central metal ion in a predefined coordination geometry. While this approach allows for ligand exchange, and captures the correct electrostatics as demonstrated for different divalent metal ions, current dummy models neglect ion-induced dipole interactions. In the present work, we resolve this weakness by taking advantage of the recently introduced 12-6-4 type Lennard-Jones potential to include ion-induced dipole interactions. We revise our previous dummy model for Mg
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