ArticleThe Journal of chemical physics2018
Implicit ligand theory for relative binding free energies.
Article in The Journal of chemical physics, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 6 papers.
What it found
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Who cites it
6 citing papers in PubMed.
- Absolute Binding Free Energy Calculations between the SARS-CoV-2 Main Protease and 130 Drug Leads Using Implicit Ligand Theory.Journal of chemical information and modeling · 2026Article
- Developing end-point methods for absolute binding free energy calculation using the Boltzmann-quasiharmonic model.Physical chemistry chemical physics : PCCP · 2022Article
- Implicit ligand theory for relative binding free energies: II. An estimator based on control variates.Journal of physics communications · 2020Article
- Alchemical Grid Dock (AlGDock): Binding Free Energy Calculations between Flexible Ligands and Rigid Receptors.Journal of computational chemistry · 2020Article
- Alchemical Grid Dock (AlGDock) calculations in the D3R Grand Challenge 3 : Binding free energies between flexible ligands and rigid receptors.Journal of computer-aided molecular design · 2019Article
- Efficiency of Stratification for Ensemble Docking Using Reduced Ensembles.Journal of chemical information and modeling · 2018Article
Corrections and comments
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Authors and funding
2 authors.
Funding
Abstract
Implicit ligand theory enables noncovalent binding free energies to be calculated based on an exponential average of the binding potential of mean force (BPMF)-the binding free energy between a flexible ligand and rigid receptor-over a precomputed ensemble of receptor configurations. In the original formalism, receptor configurations were drawn from or reweighted to the apo ensemble. Here we show that BPMFs averaged over a holo ensemble yield binding free energies relative to the reference ligand that specifies the ensemble. When using receptor snapshots from an alchemical simulation with a single ligand, the new statistical estimator outperforms the original.
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Registered trials
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