Fig. 5: Analysis of the quality of the membrane-associated protein models before and after refinement with HADDOCK.
From: Integrative modeling of membrane-associated protein assemblies
a Stacked bar plot of the top 100 generated models for each of the benchmark cases (18 in total) ranked by their respective score (left–LightDock DFIRE docking score, right-HADDOCK score). For each complex the left bar corresponds to the unrefined models and the right bar to the refined models. The color coding (from green to red) indicates the number of clashes. b Illustration of a complex before and after refinement. Green spheres represent atomic clashes. The corresponding side chains are shown as sticks in the refined model. c i-RMSD comparison of all models with an i-RMSD ≤ 6 Å before and after refinement (183 in total). Points above the diagonal indicate an improvement in i-RMSD value. Source data are provided as an excel file.
