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Full-Text Articles in Biological and Chemical Physics
Continued Development Of An Empirical Function For Predicting And Rationalizing Protein–Protein Binding Affinities, Joseph Audie
Continued Development Of An Empirical Function For Predicting And Rationalizing Protein–Protein Binding Affinities, Joseph Audie
Chemistry & Physics Faculty Publications
Here we summarize recent work on the continued development of our fast and simple empirical equation for predicting and structurally rationalizing protein–protein and protein–peptide binding affinities. Our empirical expression consists of six regression-weighted physical descriptors and derives from two key simplifying assumptions: (1) the assumption of rigid-body association and (2) the assumption that all contributions not explicitly considered in the equation make a net contribution to binding of ≈0 kcal. Within the strict framework of rigid-body association, we tested relative binding affinity predictions using our empirical equation against the corresponding experimental binding free energy data for 197 interface alanine mutants. …
Development And Validation Of An Empirical Free Energy Function For Calculating Protein–Protein Binding Free Energy Surfaces, Joseph Audie
Development And Validation Of An Empirical Free Energy Function For Calculating Protein–Protein Binding Free Energy Surfaces, Joseph Audie
Chemistry & Physics Faculty Publications
In a previous paper, we described a novel empirical free energy function that was used to accurately predict experimental binding free energies for a diverse test set of 31 protein–protein complexes to within ≈1.0 kcal. Here, we extend that work and show that an updated version of the function can be used to (1) accurately predict native binding free energies and (2) rank crystallographic, native-like and non-native binding modes in a physically realistic manner. The modified function includes terms designed to capture some of the unfavorable interactions that characterize non-native interfaces. The function was used to calculate one-dimensional binding free …