Fig. 8: Protein complex stability.

Analyses of four protein complexes simulated using ff03w-sc and ff99SBws-STQ’ force fields. The insets present the experimental structures of the complexes. A Distributions of the backbone RMSD of the full complexes. B Box plots showing the fraction of native contacts at the protein–protein interface from n = 4 independent simulations per system. Each box spans the interquartile range (IQR; 25th–75th percentile), the center line indicates the median, and whiskers extend to 1.5 × IQR; minima and maxima within this range are shown, and outliers were omitted. C Violin plots of interfacial surface area; each violin pools framewise values from n = 4 independent simulations per system. The inner box marks the median and interquartile range, and red stars indicate values from the experimental crystal structures. Source data are provided as a Source data file.