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. Author manuscript; available in PMC: 2014 Jan 1.
Published in final edited form as: Proteins. 2012 Sep 18;81(1):18–39. doi: 10.1002/prot.24150

Figure 14.

Figure 14

Examples of DEEPer GMEC searches. (a) A sequence-design run on structure 2BGX (AmiD from E. coli). The GMEC backbone moved away from the starting conformation for residues 126–131. The lack of continuous flexibility in this run allows display of all searched backbone conformations. (b) A conformational-search run on structure 2IXT (sphericase). From the starting conformation, a partial structure switch allowed the GMEC to change the backbone to that of a crystallographic alternate conformation for residues 37–42, where its sidechain rotamers also matched. Starting structure, black/gray; complete searched ensemble, purple; GMEC, pink. Green balls demarcate flexible-backbone regions; sidechains outside these regions are omitted for visual clarity.