ArticleJournal of molecular recognition : JMR2016
Parameterization of an effective potential for protein-ligand binding from host-guest affinity data.
Article in Journal of molecular recognition : JMR, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 21 papers.
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Who cites it
21 citing papers in PubMed.
- Thermodynamics of Water Displacement from Binding Sites and its Contributions to Supramolecular and Biomolecular Affinity.Angewandte Chemie (International ed. in English) · 2025Article
- Environment benign synthesis of 5-acyl-4-hydroxypyridin-2(1Future medicinal chemistry · 2024Article
- Free Energy Density of a Fluid and Its Role in Solvation and Binding.Journal of chemical theory and computation · 2024Article
- What to Make of Zero: Resolving the Statistical Noise from Conformational Reorganization in Alchemical Binding Free Energy Estimates with Metadynamics Sampling.Journal of chemical theory and computation · 2024Article
- Article
- Naphthoquinone fused diazepines targeting hyperamylasemia: potential therapeutic agents for diabetes and cancer.Future medicinal chemistry · 2024Article
- Elucidating the molecular determinants for binding modes of a third-generation HIV-1 integrase strand transfer inhibitor: Importance of side chain and solvent reorganization.bioRxiv : the preprint server for biology · 2023Article
- Developing end-point methods for absolute binding free energy calculation using the Boltzmann-quasiharmonic model.Physical chemistry chemical physics : PCCP · 2022Article
- Structure-based virtual screening workflow to identify antivirals targeting HIV-1 capsid.Journal of computer-aided molecular design · 2022Article
- Absolute Protein Binding Free Energy Simulations for Ligands with Multiple Poses, a Thermodynamic Path That Avoids Exhaustive Enumeration of the Poses.Journal of computational chemistry · 2020Article
- Role of Displacing Confined Solvent in the Conformational Equilibrium of β-Cyclodextrin.The journal of physical chemistry. B · 2019Article
- Binding Thermodynamics and Kinetics Calculations Using Chemical Host and Guest: A Comprehensive Picture of Molecular Recognition.Journal of chemical theory and computation · 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
- Computing conformational free energy differences in explicit solvent: An efficient thermodynamic cycle using an auxiliary potential and a free energy functional constructed from the end points.Journal of computational chemistry · 2017Article
- Predicting Binding Free Energies: Frontiers and Benchmarks.Annual review of biophysics · 2017Review
- Relationship between Solvation Thermodynamics from IST and DFT Perspectives.The journal of physical chemistry. B · 2017Review
- Predictions of Ligand Selectivity from Absolute Binding Free Energy Calculations.Journal of the American Chemical Society · 2017Article
- A combined treatment of hydration and dynamical effects for the modeling of host-guest binding thermodynamics: the SAMPL5 blinded challenge.Journal of computer-aided molecular design · 2017Article
- Overview of the SAMPL5 host-guest challenge: Are we doing better?Journal of computer-aided molecular design · 2017Review
- Solvation thermodynamic mapping of molecular surfaces in AmberTools: GIST.Journal of computational chemistry · 2016Article
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Authors and funding
9 authors.
Funding
Abstract
Force field accuracy is still one of the "stalemates" in biomolecular modeling. Model systems with high quality experimental data are valuable instruments for the validation and improvement of effective potentials. With respect to protein-ligand binding, organic host-guest complexes have long served as models for both experimental and computational studies because of the abundance of binding affinity data available for such systems. Binding affinity data collected for cyclodextrin (CD) inclusion complexes, a popular model for molecular recognition, is potentially a more reliable resource for tuning energy parameters than hydration free energy measurements. Convergence of binding free energy calculations on CD host-guest systems can also be obtained rapidly, thus offering the opportunity to assess the robustness of these parameters. In this work, we demonstrate how implicit solvent parameters can be developed using binding affinity experimental data and the binding energy distribution analysis method (BEDAM) and validated using the Grid Inhomogeneous Solvation Theory analysis. These new solvation parameters were used to study protein-ligand binding in two drug targets against the HIV-1 virus and improved the agreement between the calculated and the experimental binding affinities. This work illustrates how benchmark sets of high quality experimental binding affinity data and physics-based binding free energy models can be used to evaluate and optimize force fields for protein-ligand systems. Copyright © 2015 John Wiley & Sons, Ltd.
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