ArticleJournal of computer-aided molecular design2017
A combined treatment of hydration and dynamical effects for the modeling of host-guest binding thermodynamics: the SAMPL5 blinded challenge.
Article in Journal of computer-aided molecular design, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. An erratum has been issued. Cited by 8 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
8 citing papers in PubMed.
- Application of the alchemical transfer and potential of mean force methods to the SAMPL8 host-guest blinded challenge.Journal of computer-aided molecular design · 2022Article
- Role of Displacing Confined Solvent in the Conformational Equilibrium of β-Cyclodextrin.The journal of physical chemistry. B · 2019Article
- Inclusion of enclosed hydration effects in the binding free energy estimation of dopamine D3 receptor complexes.PloS one · 2019Article
- Ligand Binding Free Energies with Adaptive Water Networks: Two-Dimensional Grand Canonical Alchemical Perturbations.Journal of chemical theory and computation · 2018Article
- Overview of the SAMPL6 host-guest binding affinity prediction challenge.Journal of computer-aided molecular design · 2018Article
- Assessment of a Single Decoupling Alchemical Approach for the Calculation of the Absolute Binding Free Energies of Protein-Peptide Complexes.Frontiers in molecular biosciences · 2018Article
- Predicting Binding Free Energies: Frontiers and Benchmarks.Annual review of biophysics · 2017Review
- Overview of the SAMPL5 host-guest challenge: Are we doing better?Journal of computer-aided molecular design · 2017Review
Corrections and comments
- Erratum issued
Authors and funding
10 authors.
Funding
Abstract
As part of the SAMPL5 blinded experiment, we computed the absolute binding free energies of 22 host-guest complexes employing a novel approach based on the BEDAM single-decoupling alchemical free energy protocol with parallel replica exchange conformational sampling and the AGBNP2 implicit solvation model specifically customized to treat the effect of water displacement as modeled by the Hydration Site Analysis method with explicit solvation. Initial predictions were affected by the lack of treatment of ionic charge screening, which is very significant for these highly charged hosts, and resulted in poor relative ranking of negatively versus positively charged guests. Binding free energies obtained with Debye-Hückel treatment of salt effects were in good agreement with experimental measurements. Water displacement effects contributed favorably and very significantly to the observed binding affinities; without it, the modeling predictions would have grossly underestimated binding. The work validates the implicit/explicit solvation approach employed here and it shows that comprehensive physical models can be effective at predicting binding affinities of molecular complexes requiring accurate treatment of conformational dynamics and hydration.
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Registered trials
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