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Figure 2 | BMC Systems Biology

Figure 2

From: RaTrav: a tool for calculating mean first-passage times on biochemical networks

Figure 2

The true positive binding funnel. The true positive binding funnel for the vitamin D-binding protein/actin complex (1KXP [22]) generated with the SwarmDock Server [20] by docking unbound receptor/ligand pair included in Benchmark 4.0 [25]. The protein-protein conformational states are numbered from ID 0 to 31. The letter indicates the quality of solution in accordance to CAPRI [24] classification as: M – medium quality (blue), A – acceptable quality (green), I – incorrect solution (red). Favourable paths are marked in red. Figure created with Gephi [26] based on Example1/1KXP.gml file (Additional file 1). See text for more details.

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