Figure 1

Mapping oncogenic mutations onto the interfaces of predicted protein-protein complexes and in silico mutagenesis. Mutational data related to the proteins in the network were taken from the COSMIC database [49, 50] and The Cancer Genome Atlas, TCGA [51]. To map oncogenic mutations, we identified the interfaces of the modeled protein-protein complexes using the HotPoint web server [52]. After the mutational mapping, we performed in silico mutagenesis to observe the effects of mutations - that are on the interface - on the interactions. We computationally mutated those key residues using the FoldX plugin [53] for the YASARA molecular viewer [54]. We minimized the energies of the proteins both before and after the mutation and then used the mutant structures to re-run PRISM [35, 36] and model the new interaction between the mutant target and its partner.