*4.1. Conformational Clustering*

The conformational ensemble of the studied construct encompassing N-WASP domain V and previously generated by MD simulations with the Amber-03ws force field [29] was clustered with the GROMACS tool *gmx cluster* using the *gromos* method [35] and a RMSD cutoff of 0.5 nm (computed over the mainchain atoms). We obtained 2467 clusters and decided, for subsequent protein–protein docking calculations, to keep only the 527 most populated ones, which represent 50% of the 40,000 conformations sampled by MD simulations. To verify that the 527 clusters are representative of the overall conformational ensemble, we compared the residue probabilities to be in *α*-helix and the distributions of gyration averaged over the 40,000 conformations or the 527 cluster structures. As shown in Figure S2, the probabilities to form *α*-helices of the 527 clusters and of the whole conformational ensemble are almost identical, and the protein radius of gyration has similar distributions when computed over the sub-ensemble of representative structures or over the 40,000 conformations. This indicates that the selected 527 conformers are locally and globally representative of the whole conformational ensemble of N-WASP domain V.
