Comparison of the energy scores versus the affinities of the mutations show how well the programs reproduce the differences.

<p>For each test case with more than two mutations, we plotted the top binding scores of CADDSuite, Vina, and Rosetta designs for each mutation on each scaffold structure together with the logarithm of the affinity. Here we show plots for Carbonic anhydrase II, HIV-1 protease, and Streptavidin test 1. All other plots are shown in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0052505#pone.0052505.s001" target="_blank">Information S1</a>. Values are scaled to fit in the same range. Shown on the x-axis of a plot are the mutants in order of affinity to the ligand (the leftmost has the lowest affinity, compare <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0052505#pone-0052505-t001" target="_blank">Table 1</a> for the actual values). The y-axis measures predicted binding scores for the designs, and the log affinities, scaled between 0 and 1. Both are proportional to the binding free energy, and can therefore be compared when scaled to the same range. The lowest predicted binding score or log affinity is set to 0, the highest respective value to 1. Each plot contains a line for the affinity logarithm (solid, black no marker). This line represents the goal, if a method predicts binding well, the binding score lines should closely follow the log affinity line. The other markers and lines show the scaled predicted binding scores. One line represents the designs calculated for all available mutants, calculated by using one crystal structure as the scaffold. (Crystal structure 1: dashed, blue, circle markers; structure 2: red, dotted, square markers; structure 3: green, dash-dot pattern, diamond markers; structure 4: cyan, two dashes one dot pattern, star markers). We chose to use lines for representation, because this makes it easy to visually compare the shape of the black log affinity line to the lines representing the design binding scores. Each row has plots for one test case, in parentheses the order of scaffold structures is listed: <i>CA</i>: Carbonic anhydrase II (1ydb, 1yda, 1ydd), <i>HP</i>: HIV-1 protease (1met, 1meu, 1mes), <i>S1</i>: Streptavidin test 1 (1swe, 1n43).