Fig. 6: Improving GōMartini to match AA models.
From: GōMartini 3: From large conformational changes in proteins to environmental bias corrections
RMSF comparison between original GōMartini (with εLJ optimized), modified GōMartini (with the removal of Gō interactions in loops), and AA simulations for three proteins: titin I-band (1TIT), glycoside hydrolase (3W0K), and the transmembrane domain of Ist2. Solid lines represented the RMSF mean values; the shaded area the standard deviation (N = 2 for the AA simulations and N = 3 for the CG ones). The mean absolute error (MAE) for loops and structured regions, calculated as the average of the absolute differences between the RMSF values of GōMartini models and AA simulation, is highlighted in the insets. The bottom-right panel presents the flexibility of the protein backbone beads during simulations using the modified GōMartini model for glycoside hydrolase (3W0K). Source data are provided as a Source Data file.
