Extended Data Table 2 Interface side-chain heavy-atom RMSD calculations and SAXS Vr calculations

From: De novo design of modular peptide-binding proteins by superhelical matching

  1. a, Interface side-chain heavy-atom RMSD calculation for four co-crystal complexes and design models. The interface heavy-atom RMSD calculations using Pymol align with cycles=0 (iRMSD for short) was applied to all four crystal-design complexes. For the first-round designs, for example, the values are averaged over five top designs for RPB_PEW3_R4–PAWx4, because the design models were not fully converged (as stated in the main text). For RPB_LRP3_R4–LRPx4, because the final two models were sampling two distinct arginine rotamers as stated in the main text, we calculated the iRMSD for these two, respectively. The closest one was shown above with asterisks, and the further one as (full_iRMSD = 5.29, inter_iRMSD = 5.16). For all four pairs, we inspected both the full-repeat RMSD with internal-repeat RMSD (N-terminal and C-terminal caps excluded) here, owing to the potential lever-arm effect. b, Structural validation of six-repeat peptide binders by SAXS volatility ratio (Vr) calculation.
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