Extended Data Fig. 1: Examples of computationally designed model geometry and convergence of backbone docking.
From: De novo design of modular peptide-binding proteins by superhelical matching
a–c, Examples of repeat proteins computationally designed to bind to extended beta strand (a), polypeptide II (b) and helical peptide backbones (c). d, Monte Carlo flexible backbone docking calculations after design to assess the structural specificity of the designed peptide-binding interface. It started from large numbers of peptide conformations randomly generated with superhelical parameters in the range of those of the proteins (usually 10,000–50,000 trajectories), and selected those designs with converged peptide backbones (RMSD < 2.0 among the top 20 designs with lowest DDG) close to the design model (RMSD < 1.5). Green dots shown in the above example plot represent the converged designs picked by this threshold.
