Fig. 1: IDP optimization in Martini 3.
From: Martini3-IDP: improved Martini 3 force field for disordered proteins
Mean Rg calculated from simulations plotted against experimental Rg for A standard Martini 3 (MAE = 1.058 nm, PCC = 0.948) and B Martini3-IDP (MAE = 0.387 nm, PCC = 0.803). Rg data are presented as mean values ± statistical error estimates, error bars of experimental Rg values were determined by a fitting error from the Guinier fit and error bars of simulations represent the standard deviation of 5 blocks from blocking analysis. C Comparison of bonded distributions involving protein backbone (BB) and first side chain (SC1) beads between Martini3, Martini3-IDP and CHARMM36m. KL divergence between bonded distributions are provided in Supplementary Table 10. The distributions of CHARMM36m were obtained by mapping the AA trajectory to Martini resolution. Due to the different nature of Gly residue, BB-BB-BB-SC1 and SC1-BB-BB-BB dihedral angles involving Gly were excluded and are provided separately in Supplementary Fig. 4. BB represents the BB–BB bond length; BBB, BBS and SBB represent the BB-BB-BB, BB-BB-SC1 and SC1-BB-BB angles; BBBB, SBBS,SBBB and BBBS represent the BB-BB-BB-BB, SC1-BB-BB-SC1, SC1-BB-BB-BB and BB-BB-BB-SC1 dihedral angle, respectively.
