ArticlePhysical chemistry chemical physics : PCCP2016
Calculating binding free energies of host-guest systems using the AMOEBA polarizable force field.
Article in Physical chemistry chemical physics : PCCP, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 30 papers.
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Who cites it
30 citing papers in PubMed.
- The SAMPL9 host-guest blind challenge: an overview of binding free energy predictive accuracy.Physical chemistry chemical physics : PCCP · 2024Article
- Scalable hybrid deep neural networks/polarizable potentials biomolecular simulations including long-range effects.Chemical science · 2023Article
- Accurate Host-Guest Binding Free Energies Using the AMOEBA Polarizable Force Field.Journal of chemical information and modeling · 2023Article
- Atomic Polarizabilities for Interactive Dipole Induction Models.Journal of chemical information and modeling · 2022Article
- Computational study on the binding of Mango-II RNA aptamer and fluorogen using the polarizable force field AMOEBA.Frontiers in molecular biosciences · 2022Article
- Thermodynamics of ion binding and occupancy in potassium channels.Chemical science · 2021Article
- Automation of absolute protein-ligand binding free energy calculations for docking refinement and compound evaluation.Scientific reports · 2021Article
- Experimental characterization of the association of β-cyclodextrin and eight novel cyclodextrin derivatives with two guest compounds.Journal of computer-aided molecular design · 2021Article
- Molecular dynamics free energy simulations of ATP:MgMolecular simulation · 2021Article
- AMOEBA binding free energies for the SAMPL7 TrimerTrip host-guest challenge.Journal of computer-aided molecular design · 2021Article
- Predicting partition coefficients of drug-like molecules in the SAMPL6 challenge with Drude polarizable force fields.Journal of computer-aided molecular design · 2020Article
- Data-driven analysis of the number of Lennard-Jones types needed in a force field.Communications chemistry · 2020Article
- Molecular Dynamics Study of the Hybridization between RNA and Modified Oligonucleotides.Journal of chemical theory and computation · 2019Article
- Computational and Experimental Studies of Inhibitor Design for Aldolase A.The journal of physical chemistry. B · 2019Article
- AMOEBA+ Classical Potential for Modeling Molecular Interactions.Journal of chemical theory and computation · 2019Article
- Computational insights into the binding of IN17 inhibitors to MELK.Journal of molecular modeling · 2019Article
- Polarizable Force Fields for Biomolecular Simulations: Recent Advances and Applications.Annual review of biophysics · 2019Review
- Force field development phase II: Relaxation of physics-based criteria… or inclusion of more rigorous physics into the representation of molecular energetics.Journal of computer-aided molecular design · 2019Review
- Tinker 8: Software Tools for Molecular Design.Journal of chemical theory and computation · 2018Article
- Overview of the SAMPL6 host-guest binding affinity prediction challenge.Journal of computer-aided molecular design · 2018Article
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Authors and funding
8 authors.
Funding
Abstract
Molecular recognition is of paramount interest in many applications. Here we investigate a series of host-guest systems previously used in the SAMPL4 blind challenge by using molecular simulations and the AMOEBA polarizable force field. The free energy results computed by Bennett's acceptance ratio (BAR) method using the AMOEBA polarizable force field ranked favorably among the entries submitted to the SAMPL4 host-guest competition [Muddana, et al., J. Comput.-Aided Mol. Des., 2014, 28, 305-317]. In this work we conduct an in-depth analysis of the AMOEBA force field host-guest binding thermodynamics by using both BAR and the orthogonal space random walk (OSRW) methods. The binding entropy-enthalpy contributions are analyzed for each host-guest system. For systems of inordinate binding entropy-enthalpy values, we further examine the hydrogen bonding patterns and configurational entropy contribution. The binding mechanism of this series of host-guest systems varies from ligand to ligand, driven by enthalpy and/or entropy changes. Convergence of BAR and OSRW binding free energy methods is discussed. Ultimately, this work illustrates the value of molecular modelling and advanced force fields for the exploration and interpretation of binding thermodynamics.
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