Fig. 4.

Results for a projection of the frames obtained from the reconnaissance metadynamics simulations of ala12. The parameters of the sigmoid functions were chosen to be σ = 6, a_D = b_D = 12, a_d = 1, and b_d = 2. Points not included in the landmark set were embedded with the out-of-sample extension described in the text. The 2D projection is shown, with the embedded points colored in accordance with the number of residues that, according to STRIDE, are part of an alpha helix or beta sheet. A key for the color scheme is also shown, together with snapshots of a few selected configurations.