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. Author manuscript; available in PMC: 2016 Mar 23.
Published in final edited form as: Proteins. 2006 Nov 15;65(3):712–725. doi: 10.1002/prot.21123

Figure 4.

Figure 4

“Lowest energy” profiles for three prototypical decoy systems, each tested with six AMBER force field variants (ff94, ff99, ff99SB, ff03, ff94gs, ff99ϕ): (A) trpzip2, which is known to adopt a β-hairpin, (B) a Baldwin-type sequence as a representative of an α-helix, and (C) trpcage as a representative of mixed secondary structures. RMSD values are calculated using the experimentally determined structure as a reference. Ideally, a force field should show lowest energies for the lowest RMSD values.