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. Author manuscript; available in PMC: 2015 Dec 1.
Published in final edited form as: Proteins. 2014 Oct 30;82(12):3255–3272. doi: 10.1002/prot.24658

Figure 8.

Figure 8

Examples of residue-wise energies by SDE and other potentials. Two decoy sets included in the Lmds set, 1fc2 and 1bba, were used. As shown in Table V, SDE and MRE successfully identified the native structure among 501 decoys for these two decoy sets. A to E are comparison between the SDE and GOAP energies at individual residues in the native structure of 1fc2 and the lowest GOAP energy decoy, 1fc2.60276.pdb. F to H are comparison between the SDE and DFIRE energies at each residue in the native of 1bba and the lowest DFIRE energy decoy, 1bba.1697.pdb. (A) Energy difference at each residue between the native 1fc2 and the decoy 1fc2.60276.pdb by GOAP, DFIRE, MRE, and SDE. The y-axis shows the residue-wise energy difference between the native and the decoy. A negative value indicates that the residue has a lower energy in the native than the decoy. SDE and MRE scores are negated so that they have the same sign as the other two potentials. (B) The structure of the decoy 1fc2.60276.pdb. ILE12 is shown in red, and three residues that have preferable GOAP energy between 1LE12, namely, PHE26, LEU30, and LEU41 are shown in yellow, green, and cyan, respectively. (C) The native structure of 1fc2. ILE12, PHE26, LEU30, and LEU41 are shown in the same colors as in the panel B. (D) The pairwise GOAP energies between ILE12 and the other residues in the decoy 1fc2.60276.pdb. (E) The Euclidean distance of side-chain centroids of each residue in the native and the decoy after the two structures are superimposed by the LGA program. A high distance (y-axis) indicates that the residue position in the decoy is far off from its correct position. (F) Energy difference at each residue between the native 1bba and the decoy 1bba.1697.pdb by GOAP, DFIRE, MRE, and SDE. (G) Superimposition of the native structure (pink) of 1bba and the decoy 1bba.1697.pdb (cyan). LEU24 are shown in the stick representation in red and blue in the native and the decoy, respectively. (H) Pairwise DFIRE energies between LEU24 and each residue in the native (filled circles) and in the decoy 1bba.1697.pdb (open circles).