Fig. 7: Improving IDP global dimensions and condensation using Martini 3 with GōMartini model-based interaction rescaling.
From: GōMartini 3: From large conformational changes in proteins to environmental bias corrections
A Radii of gyration of the IDP benchmark set of Thomasen et al. Results are compared between the experimental value (blue) to both the native Martini model (purple) and optimized Martini IDP + Gō model with additional bonded parameters (green). For the experimental data, the error bars indicate the experimental uncertainty taken from ref. 47. B Illustrations of the increase in ensemble dimensions of ACTR comparing (left) native Martini 3 and (right) the final model for IDPs with additional bonded and non-bonded potentials. C, D Illustrative snapshots of a condensate (with improved IDP parameters) and an aggregate (with default Martini 3 parameters) of an artificial IDP (WT20) known to phase separate. E Snapshots of FLssLF peptide systems with varying increases in the strength of the BB-water interactions. Left; native Martini (0% increase); middle: 6% increase; right: 8% increase of protein BB-water interactions. Source data are provided as a Source Data file.
