ArticleJournal of chemical theory and computation2013
Calculating the sensitivity and robustness of binding free energy calculations to force field parameters.
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 16 papers.
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Who cites it
16 citing papers in PubMed.
- Bayesian Modeling of Polarizable Water: Lessons for Force Field Development.Journal of chemical theory and computation · 2026Article
- Developing and Benchmarking Sage 2.3.0 with the AshGC Neural Network Charge Model.Journal of chemical theory and computation · 2026Article
- Stability-Driven Pose Prediction and Ligand Design via Contact Persistence Analysis from Molecular Dynamics Simulations.Computational and structural biotechnology journal · 2026Article
- Quantification of the Impact of Structure Quality on Predicted Binding Free Energy Accuracy.Journal of chemical information and modeling · 2025Article
- Optimal Dielectric Boundary for Binding Free Energy Estimates in the Implicit Solvent.Journal of chemical information and modeling · 2024Article
- The Open Force Field Initiative: Open Software and Open Science for Molecular Modeling.The journal of physical chemistry. B · 2024Article
- Global Optimization of the Lennard-Jones Parameters for the Drude Polarizable Force Field.Journal of chemical theory and computation · 2021Article
- Multidimensional Global Optimization and Robustness Analysis in the Context of Protein-Ligand Binding.Journal of chemical theory and computation · 2020Article
- Optimized Lennard-Jones Parameters for Druglike Small Molecules.Journal of chemical theory and computation · 2018Article
- Quantitative Assessment of the Energetics of Dopamine Translocation by Human Dopamine Transporter.The journal of physical chemistry. B · 2018Article
- Accurate calculation of the absolute free energy of binding for drug molecules.Chemical science · 2016Article
- Protein-Ligand Electrostatic Binding Free Energies from Explicit and Implicit Solvation.Journal of chemical theory and computation · 2015Article
- Assessing the potential of atomistic molecular dynamics simulations to probe reversible protein-protein recognition and binding.Scientific reports · 2015Article
- Extensive all-atom Monte Carlo sampling and QM/MM corrections in the SAMPL4 hydration free energy challenge.Journal of computer-aided molecular design · 2014Article
- Fragment-based error estimation in biomolecular modeling.Drug discovery today · 2014Review
- One Size Does Not Fit All: The Limits of Structure-Based Models in Drug Discovery.Journal of chemical theory and computation · 2013Article
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3 authors.
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Abstract
Binding free energy calculations offer a thermodynamically rigorous method to compute protein-ligand binding, and they depend on empirical force fields with hundreds of parameters. We examined the sensitivity of computed binding free energies to the ligand's electrostatic and van der Waals parameters. Dielectric screening and cancellation of effects between ligand-protein and ligand-solvent interactions reduce the parameter sensitivity of binding affinity by 65%, compared with interaction strengths computed in the gas-phase. However, multiple changes to parameters combine additively on average, which can lead to large changes in overall affinity from many small changes to parameters. Using these results, we estimate that random, uncorrelated errors in force field nonbonded parameters must be smaller than 0.02 e per charge, 0.06 Å per radius, and 0.01 kcal/mol per well depth in order to obtain 68% (one standard deviation) confidence that a computed affinity for a moderately-sized lead compound will fall within 1 kcal/mol of the true affinity, if these are the only sources of error considered.
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