Figure 2.

Basic structure of Rosetta's low-resolution protocol (see Ref. 5 for full details). The search progresses through four stages, which use different scoring functions. The knowledge-based scoring function combines 10 different terms, which are progressively activated (and up-weighted) as the search progresses. Stages 1–3 use fragments covering nine residues, while the last stage uses fragments covering three residues. The term vdw captures steric repulsion. The statistical potential consists of the terms env and pair, which capture the residue environment and residue pair interactions, respectively. Furthermore, there are four terms that describe interactions between secondary structure elements (ss_pair, hs_pair, sheet, and rsigma) and three terms related to the density and compactness of structures (cbeta, cenpack, and rg). See Table I in Ref. 5 for more details. [Color figure can be viewed in the online issue, which is available at wileyonlinelibrary.com.]