Figure 1.
RosettaDock is a multi-scale Monte-Carlo based algorithm that roughly models encounter complex formation followed by a transition to a bound state.
Table 1.
RosettaDock scoring components and weights.
Figure 2.
Structure of major classes associated with docking.
A shaded diamond indicates composition (the object the diamond points towards is responsible for the lifecycle of the other object); an open diamond indicates aggregation (the object the diamond points towards has an instance of the other object but it may not be solely responsible for that instance's lifecycle); and an open triangle indicates a class hierarchy with the triangle pointing towards the parent class.
Figure 3.
Examples of docking successes and failures.
Interface energy vs. I_rmsd scatter plots for representative cases of (A) a docking success, (B) RB-sampling failure, (C) BB-sampling failure, and (D) a discrimination failure. Standard docking run decoys are in gray, the ten lowest-energy decoys from refinement of the unbound conformers superimposed on the native complex are in green, and the ten lowest-energy decoys from refinement of the bound complex is in red.
Figure 4.
Breakdown of benchmark results.
The RosettaDock benchmark performance in terms of docking success and accuracy across both complex type (A) and docking difficulty (B).
Table 2.
Docking Benchmark 3.0 results summary for successes.
Table 3.
Docking Benchmark 3.0 results summary for failures.
Table 4.
Docking success and failure by complex type and difficulty.
Figure 5.
Comparison of RosettaDock v3.2 and RosettaDock v2.3.
A histogram showing the docking success and accuracy for a benchmark set of 116 targets for the new RosettaDock v3.2 and the older RosettaDock v2.3.
Figure 6.
Docking of the FNR-Fn ternary complex.
Plots of score vs. Lrmsd for local docking of the unbound structures in target 1EWY without (A) and with (B) the small molecule FAD bound to FNR (A), with high, medium, and acceptable accuracy decoys colored in brown, orange, and tan, respectively. (C) The second-lowest energy structure from docking using FAD with FNR (green), Fd (cyan), and the FAD molecule (magenta) superimposed on the crystal structure of the complex (gray).
Table 5.
Results of incorporating small molecules in Rosetta v3.2.