Interpreting the effect of mutations to protein binding sites from large-scale genomic screens

[Display omitted] •Binding energies can be calculated for missense mutations to protein binding sites.•Calculating all possible mutations to protein binding sites generates an energy distribution.•Comparison of the distribution to groups of mutations allows statistical comparisons.•Energy distributions can be compared to other data types such as clinical data.•Energy distributions can be used to predict mutation functionality. Predicting the functionality of missense mutations is extremely difficult. Large-scale genomic screens are commonly performed to identify mutational correlates or drivers of disease and treatment resistance, but interpretation of how these mutations impact protein function is limited. One such consequence of mutations to a protein is to impact its ability to bind and interact with partners or small molecules such as ATP, thereby modulating its function. Multiple methods exist for predicting the impact of a single mutation on protein–protein binding energy, but it is difficult in the context of a genomic screen to understand if these mutations with large impacts on binding are more common than statistically expected. We present a methodology for taking mutational data from large-scale genomic screens and generating functional and statistical insights into their role in the binding of proteins both with each other and their small molecule ligands. This allows a quantitative and statistical analysis to determine whether mutations impacting protein binding or ligand interactions are occurring more or less frequently than expected by chance. We achieve this by calculating the potential impact of any possible mutation and comparing an expected distribution to the observed mutations. This method is applied to examples demonstrating its ability to interpret mutations involved in protein–protein binding, protein-DNA interactions, and the evolution of therapeutic resistance.