Induced fit with replica exchange improves protein complex structure prediction
Fig 4
Comparison of performance metrics between RosettaDock 4.0 and ReplicaDock 2.0 for individual complexes in a benchmark set of 88 docking targets.
(A) Comparison of 〈N5〉 values after low-resolution and high-resolution stages (full protocol), respectively. Dashed lines highlight the region in which the two protocols differ significantly, i.e. by more than one point in their 〈N5〉 values. Different symbols correspond to each target’s difficulty category (circle: rigid; triangle: medium; diamond: flexible). Points above the solid line represent better performance in ReplicaDock 2.0, while points below the line represent better performance in RosettaDock 4.0. After the full protocol, 24 targets are modeled significantly better and 14 complexes are modeled significantly worse. (B) Probability density curves versus 〈N5〉 for all targets for ReplicaDock 2.0 (green) and RosettaDock 4.0 (purple). Low-resolution performance is indicated by lines (bright pink and bright green), and high-resolution performance is denoted by shaded area (purple and green). (C) Probability density curves versus full-protocol average N5 for rigid, medium and flexible targets respectively.