ArticleJournal of chemical theory and computation2013
Standard binding free energies from computer simulations: What is the best strategy?
Article in Journal of chemical theory and computation, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 120 papers.
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Who cites it
120 citing papers in PubMed, 353 citations in OpenAlex.
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- Free energy simulations on a biomimetic glucose receptor: understanding the selectivity of GluHUT.Chemical science · 2026Article
- Assessing Computational Strategies for the Evaluation of Antibody Binding Affinities.Journal of chemical theory and computation · 2025Article
- On Free Energy Calculations in Drug Discovery.Accounts of chemical research · 2025Article
- Efficient and accurate binding free energy calculation of AβProteins · 2025Article
- Binding Free Energy Calculations Based on the Path Collective Variable along a String Pathway.The journal of physical chemistry. B · 2025Article
- Thermodynamics of arginine interactions with organic phosphates.Biophysical journal · 2025Article
- Multiscale Computational Protocols for Accurate Residue Interactions at the Flexible Insulin-Receptor Interface.Journal of chemical information and modeling · 2025Article
- Applying Absolute Free Energy Perturbation Molecular Dynamics to Diffusively Binding Ligands.Journal of chemical theory and computation · 2025Article
- Multisite λ-Dynamics for Protein-DNA Binding Affinity Prediction.Journal of chemical theory and computation · 2025Article
- Assessment of the Topology and Oligomerisation States of Coiled Coils Using Metadynamics with Conformational Restraints.Journal of chemical theory and computation · 2025Article
- A claudin5-binding peptide enhances the permeability of the blood-brain barrier in vitro.Science advances · 2025Article
- Analysis of the Dynamics of a Complex, Multipathway Reaction: Insulin Dimer Dissociation.The journal of physical chemistry. B · 2024Article
- Expanded Functionality and Portability for the Colvars Library.The journal of physical chemistry. B · 2024Article
- Tutorial on Umbrella Sampling Simulation with a Combined QM/MM Potential: The Potential of Mean Force for an SThe journal of physical chemistry. B · 2024Article
- Advanced computational approaches to understand protein aggregation.Biophysics reviews · 2024Review
- Orientation and Membrane Partition Free Energy of PeT-Based Voltage-Sensitive Dyes from Molecular Simulations.The journal of physical chemistry. B · 2024Article
- A Rigorous Framework for Calculating Protein-Protein Binding Affinities in Membranes.Journal of chemical theory and computation · 2023Article
60 more citing papers are in PubMed but not listed here.
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Authors and funding
3 authors at 2 institutions in 2 countries.
Funding
Abstract
Accurate prediction of standard binding free energies describing protein:ligand association remains a daunting computational endeavor. This challenge is rooted to a large extent in the considerable changes in conformational, translational and rotational entropies underlying the binding process that atomistic simulations cannot easily capture. In spite of significant methodological advances, reflected in a continuously improving agreement with experiment, a characterization of alternate strategies aimed at measuring binding affinities, notably their respective advantages and drawbacks, is somewhat lacking. Here, two distinct avenues to determine the standard binding free energy are compared in the case of a short, proline-rich peptide associating to the Src homology domain 3 of tyrosine kinase Abl. These avenues - one relying upon alchemical transformations and the other on potentials of mean force (PMFs) - invoke a series of geometrical restraints acting on collective variables designed to alleviate sampling limitations inherent to classical molecular dynamics simulations. The experimental binding free energy of Δ
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