ArticleThe Journal of chemical physics2012
Implicit ligand theory: rigorous binding free energies and thermodynamic expectations from molecular docking.
Article in The Journal of chemical physics, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 15 papers.
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Who cites it
15 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
- PopShift: A Thermodynamically Sound Approach to Estimate Binding Free Energies by Accounting for Ligand-Induced Population Shifts from a Ligand-Free Markov State Model.Journal of chemical theory and computation · 2024Article
- 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
- Middle-way flexible docking: Pose prediction using mixed-resolution Monte Carlo in estrogen receptor α.PloS one · 2019Article
- 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
- Simple Entropy Terms for End-Point Binding Free Energy Calculations.Journal of chemical theory and computation · 2018Article
- Efficiency of Stratification for Ensemble Docking Using Reduced Ensembles.Journal of chemical information and modeling · 2018Article
- Power transformations improve interpolation of grids for molecular mechanics interaction energies.Journal of computational chemistry · 2018Article
- Using the fast fourier transform in binding free energy calculations.Journal of computational chemistry · 2018Article
- Implicit ligand theory for relative binding free energies.The Journal of chemical physics · 2018Article
- Systematic Testing of Belief-Propagation Estimates for Absolute Free Energies in Atomistic Peptides and Proteins.Journal of chemical theory and computation · 2018Article
- Hamiltonian Monte Carlo with Constrained Molecular Dynamics as Gibbs Sampling.Journal of chemical theory and computation · 2017Article
- Absolute Binding Free Energies between T4 Lysozyme and 141 Small Molecules: Calculations Based on Multiple Rigid Receptor Configurations.Journal of chemical theory and computation · 2017Article
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Abstract
A rigorous formalism for estimating noncovalent binding free energies and thermodynamic expectations from calculations in which receptor configurations are sampled independently from the ligand is derived. Due to this separation, receptor configurations only need to be sampled once, facilitating the use of binding free energy calculations in virtual screening. Demonstrative calculations on a host-guest system yield good agreement with previous free energy calculations and isothermal titration calorimetry measurements. Implicit ligand theory provides guidance on how to improve existing molecular docking algorithms and insight into the concepts of induced fit and conformational selection in noncovalent macromolecular recognition.
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