ArticleJournal of chemical theory and computation2015
Problems of robustness in Poisson-Boltzmann binding free energies.
Article in Journal of chemical theory and computation, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 11 papers.
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Who cites it
11 citing papers in PubMed.
- Optimal Dielectric Boundary for Binding Free Energy Estimates in the Implicit Solvent.Journal of chemical information and modeling · 2024Article
- Computational modeling of protein conformational changes - Application to the opening SARS-CoV-2 spike.Journal of computational physics · 2021Article
- Computational Design of PDZ-Peptide Binding.Methods in molecular biology (Clifton, N.J.) · 2021Article
- Multidimensional Global Optimization and Robustness Analysis in the Context of Protein-Ligand Binding.Journal of chemical theory and computation · 2020Article
- Accuracy Comparison of Generalized Born Models in the Calculation of Electrostatic Binding Free Energies.Journal of chemical theory and computation · 2018Article
- Grid-Based Surface Generalized Born Model for Calculation of Electrostatic Binding Free Energies.Journal of chemical information and modeling · 2017Article
- A Simple PB/LIE Free Energy Function Accurately Predicts the Peptide Binding Specificity of the Tiam1 PDZ Domain.Frontiers in molecular biosciences · 2017Article
- Electrostatic component of binding energy: Interpreting predictions from poisson-boltzmann equation and modeling protocols.Journal of computational chemistry · 2016Article
- Reconciling the understanding of 'hydrophobicity' with physics-based models of proteins.Journal of physics. Condensed matter : an Institute of Physics journal · 2016Review
- Examining the assumptions underlying continuum-solvent models.Journal of chemical theory and computation · 2015Article
- Protein-Ligand Electrostatic Binding Free Energies from Explicit and Implicit Solvation.Journal of chemical theory and computation · 2015Article
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Authors and funding
3 authors.
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Abstract
Although models based on the Poisson–Boltzmann (PB) equation have been fairly successful at predicting some experimental quantities, such as solvation free energies (ΔG), these models have not been consistently successful at predicting binding free energies (ΔΔG). Here we found that ranking a set of protein–protein complexes by the electrostatic component (ΔΔGel) of ΔΔG was more difficult than ranking the same molecules by the electrostatic component (ΔGel) of ΔG. This finding was unexpected because ΔΔGel can be calculated by combining estimates of ΔGel for the complex and its components with estimates of the ΔΔGel in vacuum. One might therefore expect that if a theory gave reliable estimates of ΔGel, then its estimates of ΔΔGel would be reliable. However, ΔΔGel for these complexes were orders of magnitude smaller than ΔGel, so although estimates of ΔGel obtained with different force fields and surface definitions were highly correlated, similar estimates of ΔΔGel were often not correlated.
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