Figure 1

Secondary structure illustration of the NMR structure of 1L2Y comparing with the best structure (left) found in the simulations. On the right we show the first misfolded structure [#7 in Table ] which lacks both secondary helix and trp cage.Reuse & Permissions

Figure 2

Total (top) and effective (bottom) energy of the STUN simulation resulting in the estimate of the global optimum of 1L2Y in PFF01. The horizontal axis gives the number of steps in 1000 s, the total energy is given in $\mathrm{k}\mathrm{c}\mathrm{a}\mathrm{l}/\mathrm{m}\mathrm{o}\mathrm{l}$, the effective energy is dimensionless. The arrows indicate the configurations analyzed in Fig. 3.Reuse & Permissions

Figure 3

Illustration of the degree of similarity of successive local minima in a STUN simulation of 1L2Y. Each row represents a different structure along the simulation pathway: the bottom/top rows represent the initial/final structures, with all local minima [defined by the end of a cooling cycle, see arrows in Fig. 2] in between. Color codes indicate the similarity to all previous structures: white squares represent identity, light shade close structures ($\mathrm{R}\mathrm{M}\mathrm{S}\mathrm{B}<1\AA$), medium shade similar structures ($1\AA <\mathrm{R}\mathrm{M}\mathrm{S}\mathrm{B}<2.5\AA$), and dark shade relatively different structures ($2.5\AA <\mathrm{R}\mathrm{M}\mathrm{S}\mathrm{B}$). Dark areas in the off diagonal indicate that the simulation explored very different regions of phase space, lighter areas (e.g., top right corner) indicate that the simulation returned to an area of phase space it had visited before.Reuse & Permissions