ArticleJournal of chemical theory and computation2012
Calculation of Host-Guest Binding Affinities Using a Quantum-Mechanical Energy Model.
Article in Journal of chemical theory and computation, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 23 papers.
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Who cites it
23 citing papers in PubMed.
- Computation of Protein-Ligand Binding Free Energies with a Quantum Mechanics-Based Mining Minima Algorithm.Journal of chemical theory and computation · 2025Article
- Computation of host-guest binding free energies with a new quantum mechanics based mining minima algorithm.The Journal of chemical physics · 2021Article
- Recent Developments and Applications of the MMPBSA Method.Frontiers in molecular biosciences · 2017Review
- Blinded predictions of host-guest standard free energies of binding in the SAMPL5 challenge.Journal of computer-aided molecular design · 2017Article
- Stochastic level-set variational implicit-solvent approach to solute-solvent interfacial fluctuations.The Journal of chemical physics · 2016Article
- Recent Progress in Treating Protein-Ligand Interactions with Quantum-Mechanical Methods.International journal of molecular sciences · 2016Review
- Semiempirical Quantum Mechanical Methods for Noncovalent Interactions for Chemical and Biochemical Applications.Chemical reviews · 2016Review
- Parameterization of an effective potential for protein-ligand binding from host-guest affinity data.Journal of molecular recognition : JMR · 2016Article
- Binding enthalpy calculations for a neutral host-guest pair yield widely divergent salt effects across water models.Journal of chemical theory and computation · 2015Article
- LS-VISM: A software package for analysis of biomolecular solvation.Journal of computational chemistry · 2015Article
- Enhanced semiempirical QM methods for biomolecular interactions.Computational and structural biotechnology journal · 2015Review
- Bridging Calorimetry and Simulation through Precise Calculations of Cucurbituril-Guest Binding Enthalpies.Journal of chemical theory and computation · 2014Article
- Quantum Mechanical Calculation of Noncovalent Interactions: A Large-Scale Evaluation of PMx, DFT, and SAPT Approaches.Journal of chemical theory and computation · 2014Article
- Variational Implicit Solvation with Poisson-Boltzmann Theory.Journal of chemical theory and computation · 2014Article
- The SAMPL4 host-guest blind prediction challenge: an overview.Journal of computer-aided molecular design · 2014Review
- Blind prediction of SAMPL4 cucurbit[7]uril binding affinities with the mining minima method.Journal of computer-aided molecular design · 2014Article
- A third-generation dispersion and third-generation hydrogen bonding corrected PM6 method: PM6-D3H+.PeerJ · 2014Article
- Variational Implicit-Solvent Modeling of Host-Guest Binding: A Case Study on Cucurbit[7]uril|Journal of chemical theory and computation · 2013Article
- Large scale affinity calculations of cyclodextrin host-guest complexes: Understanding the role of reorganization in the molecular recognition process.Journal of chemical theory and computation · 2013Article
- Quantum Mechanics Approaches to Drug Research in the Era of Structural Chemogenomics.International journal of quantum chemistry · 2013Article
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Authors and funding
2 authors.
Funding
Abstract
The prediction of protein-ligand binding affinities is of central interest in computer-aided drug discovery, but it is still difficult to achieve a high degree of accuracy. Recent studies suggesting that available force fields may be a key source of error motivate the present study, which reports the first mining minima (M2) binding affinity calculations based on a quantum mechanical energy model, rather than an empirical force field. We apply a semi-empirical quantum-mechanical energy function, PM6-DH+, coupled with the COSMO solvation model, to 29 host-guest systems with a wide range of measured binding affinities. After correction for a systematic error, which appears to derive from the treatment of polar solvation, the computed absolute binding affinities agree well with experimental measurements, with a mean error 1.6 kcal/mol and a correlation coefficient of 0.91. These calculations also delineate the contributions of various energy components, including solute energy, configurational entropy, and solvation free energy, to the binding free energies of these host-guest complexes. Comparison with our previous calculations, which used empirical force fields, point to significant differences in both the energetic and entropic components of the binding free energy. The present study demonstrates successful combination of a quantum mechanical Hamiltonian with the M2 affinity method.
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Registered trials
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