File:Symmetric oligomer design with RFdiffusion.webp

English: "A) Due to the (near-perfect - see Supplementary Methods 3.1) equivariance properties of RFdiffusion, X0 predictions from symmetric inputs are also symmetric, even at very early timepoints (and becoming increasingly symmetric through time; r.m.s.d. vs symmetrized: t = 200 1.20 Å; t = 150 0.40 Å; t = 50 0.06 Å; t = 0 0.02Å). Gray: symmetrized (top left) subunit; colors: RFdiffusion X0 prediction. B) In silico success rates for symmetric oligomer designs of various cyclic and dihedral symmetries. In silico success is defined here as the proportion of designs for which AF2 yields a prediction from a single sequence that has mean pLDDT > 80 and backbone r.m.s.d. over the oligomer between the design model and AF2 < 2Å. Note that 16 sequences per RFdiffusion design were sampled. C) Box plots of the distribution of backbone r.m.s.d.s between AF2 and the RFdiffusion design model with and without the use of external potentials during the trajectory. The external potentials used are the ‘inter-chain’ contact potential (pushing chains together), as well as the ‘intra-chain’ contact potential (making chains more globular). Using these potentials dramatically improves in silico success (Two-proportion z-test of in silico success rate: n = 100 designs per condition, z = 4.3, p = 1.9e-5). D) Designs are diverse with respect to the training dataset (the PDB). While the monomers (typically 60–100 AA) show reasonable alignment to the PDB (median 0.72), the whole oligomeric assemblies showed little resemblance to the PDB (median 0.50). E) Additional examples of design models (left) against AF2 predictions (right) for C3, C5, C12, and D4 symmetric designs (the symmetries not displayed in Fig. 3) with backbone r.m.s.d.s (Å) against their AF2 predictions of 0.82, 0.63, 0.79, and 0.78 with total amino acids 750, 900, 960, 640. F) Additional nsEM data for symmetric designs. The model is shown on the left and the 2D class averages on the right for each design. G) Two orthogonal side views of HE0537 by cryo-EM. Representative 2D class averages from the cryo-EM data are shown to the right of 2D projection images of the computational design model (lowpass filtered to 8 Å), which appear nearly identical to the experimental data. Scale bars shown (white) are 60 Å. Boxplot represents median ± IQR; tails: min/max excluding outliers (±1.5xIQR)."