ArticleJournal of chemical theory and computation2018
Simple Entropy Terms for End-Point Binding Free Energy Calculations.
Article in Journal of chemical theory and computation, 2018. 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.
- Residue-Level Affinity Decomposition via Quantum Electron Density: A Multivariable Framework Applied to HIV-1 Protease Inhibitors.The journal of physical chemistry. B · 2026Article
- BindFlow: A Free, User-Friendly Pipeline for Absolute Binding Free Energy Calculations Using Free Energy Perturbation or MM(PB/GB)SA.Journal of chemical theory and computation · 2026Article
- Ligand Reorganization for End-Point Binding Free Energy Calculations: Identifying Preferred Poses of Fentanyls in the μ Opioid Receptor.Journal of chemical theory and computation · 2025Article
- Structure optimization and molecular dynamics studies of new tumor-selectiveJournal of enzyme inhibition and medicinal chemistry · 2024Article
- Conserved Conformational Dynamics Reveal a Key Dynamic Residue in the Gatekeeper Loop of Human Cyclophilins.The journal of physical chemistry. B · 2023Article
- Elucidation of a dynamic interplay between a beta-2 adrenergic receptor, its agonist, and stimulatory G protein.Proceedings of the National Academy of Sciences of the United States of America · 2023Article
- The performance of ensemble-based free energy protocols in computing binding affinities to ROS1 kinase.Scientific reports · 2022Article
- Developing end-point methods for absolute binding free energy calculation using the Boltzmann-quasiharmonic model.Physical chemistry chemical physics : PCCP · 2022Article
- Review
- On the Use of Interaction Entropy and Related Methods to Estimate Binding Entropies.Journal of chemical theory and computation · 2021Article
- Enthalpy-Entropy Compensation in Biomolecular Recognition: A Computational Perspective.ACS omega · 2021Review
- Recent Developments in Free Energy Calculations for Drug Discovery.Frontiers in molecular biosciences · 2021Review
- On the polarization of ligands by proteins.Physical chemistry chemical physics : PCCP · 2020Article
- On Restraints in End-Point Protein-Ligand Binding Free Energy Calculations.Journal of computational chemistry · 2020Article
- Calculating the absolute binding free energy of the insulin dimer in an explicit solvent.RSC advances · 2020Article
Corrections and comments
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Authors and funding
5 authors.
Funding
Abstract
We introduce a number of computationally inexpensive modifications to the MM/PBSA and MM/GBSA estimators for binding free energies, which are based on average receptor-ligand interaction energies in simulations of a noncovalent complex, to improve the treatment of entropy: second- and higher-order terms in a cumulant expansion and a confining potential on ligand external degrees of freedom. We also consider a filter for snapshots where ligands have drifted from the initial binding pose. The variations were tested on six sets of systems for which binding modes and free energies have previously been experimentally determined. For some data sets, none of the tested estimators led to results significantly correlated with measured free energies. In data sets with nontrivial correlation, a ligand RMSD cutoff of 3 Å and a second-order truncation of the cumulant expansion was found to be comparable or better than the average interaction energy by several statistical metrics.
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Registered trials
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