ArticleJournal of chemical theory and computation2010
The Binding Energy Distribution Analysis Method (BEDAM) for the Estimation of Protein-Ligand Binding Affinities.
Article in Journal of chemical theory and computation, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 84 papers.
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Who cites it
84 citing papers in PubMed.
- An Automated Workflow for Diagnosing Sampling Issues Caused by Slow Torsional Motions in Molecular Simulations.Journal of chemical information and modeling · 2026Article
- A Quantum Framework for Protein Binding-Site Structure Prediction on Utility-Level Quantum Processors.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2026Article
- Potential distribution theory of alchemical transfer.The Journal of chemical physics · 2025Article
- Kinetics-Based State Definitions for Discrete Binding Conformations of T4 L99A in MD via Markov State Modeling.Journal of chemical information and modeling · 2024Article
- Accurate prediction of dynamic protein-ligand binding using P-score ranking.Journal of computational chemistry · 2024Article
- 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
- Prediction of protein-ligand binding affinity via deep learning models.Briefings in bioinformatics · 2024Review
- A generalized Kirkwood implicit solvent for the polarizable AMOEBA protein model.The Journal of chemical physics · 2023Article
- General Theory of Specific Binding: Insights from a Genetic-Mechano-Chemical Protein Model.Molecular biology and evolution · 2022Article
- Single Point Mutation and Its Role in Specific Pathogenicity to Reveal the Mechanism of Related Protein Families.Microbiology spectrum · 2022Article
- Modified Hamiltonian in FEP Calculations for Reducing the Computational Cost of Electrostatic Interactions.Journal of chemical information and modeling · 2022Article
- Structure-based virtual screening workflow to identify antivirals targeting HIV-1 capsid.Journal of computer-aided molecular design · 2022Article
- 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
- Computational drug design of novel COVID-19 inhibitor.Bulletin of the National Research Centre · 2022Article
- Free Energy-Based Computational Methods for the Study of Protein-Peptide Binding Equilibria.Methods in molecular biology (Clifton, N.J.) · 2022Article
- On the polarization of ligands by proteins.Physical chemistry chemical physics : PCCP · 2020Article
- Combining Alchemical Transformation with a Physical Pathway to Accelerate Absolute Binding Free Energy Calculations of Charged Ligands to Enclosed Binding Sites.Journal of chemical theory and computation · 2020Article
- Ligand Binding Thermodynamic Cycles: Hysteresis, the Locally Weighted Histogram Analysis Method, and the Overlapping States Matrix.Journal of chemical theory and computation · 2020Article
- 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
- Bioinformatics and Biosimulations as Toolbox for Peptides and Peptidomimetics Design: Where Are We?Frontiers in molecular biosciences · 2020Review
24 more citing papers are in PubMed but not listed here.
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3 authors.
Funding
Abstract
The Binding Energy Distribution Analysis Method (BEDAM) for the computation of receptor-ligand standard binding free energies with implicit solvation is presented. The method is based on a well established statistical mechanics theory of molecular association. It is shown that, in the context of implicit solvation, the theory is homologous to the test particle method of solvation thermodynamics with the solute-solvent potential represented by the effective binding energy of the protein-ligand complex. Accordingly, in BEDAM the binding constant is computed by means of a weighted integral of the probability distribution of the binding energy obtained in the canonical ensemble in which the ligand is positioned in the binding site but the receptor and the ligand interact only with the solvent continuum. It is shown that the binding energy distribution encodes all of the physical effects of binding. The balance between binding enthalpy and entropy is seen in our formalism as a balance between favorable and unfavorable binding modes which are coupled through the normalization of the binding energy distribution function. An efficient computational protocol for the binding energy distribution based on the AGBNP2 implicit solvent model, parallel Hamiltonian replica exchange sampling and histogram reweighting is developed. Applications of the method to a set of known binders and non-binders of the L99A and L99A/M102Q mutants of T4 lysozyme receptor are illustrated. The method is able to discriminate without error binders from non-binders, and the computed standard binding free energies of the binders are found to be in good agreement with experimental measurements. Analysis of the results reveals that the binding affinities of these systems reflect the contributions from multiple conformations spanning a wide range of binding energies.
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