Figure 3

Near-native docking configurations identified by LZerD for unbound-unbound complexes. Top ranking hits are shown for A, tissue factor with inhibitory Fab. The PDB ID of bound complex: 1AHW; unbound structures: 1FGN_LH (RMSD to bound structure: 1.25 Å) & 1TFH_A(RMSD: 0.75 Å). iRMSD of the prediction shown is 1.34 Å, which is ranked fifth. B, uracil-DNA glycosylase with uracil glycosylase inhibitor protein complex. Bound: 1UDI. Unbound structures: 1UDH (RMSD to bound: 0.47 Å) & 2UGI_B (RMSD: 0.88 Å). iRMSD: 2.36 Å, Rank: 59. C, Ras-RasGAP complex. Bound: 1WQ1. Unbound structures: 6Q21_D (RMSD: 0.79 Å) &1WER (RMSD: 0.85 Å). iRMSD: 1.87 Å; Rank: 141. D. T-cell receptor β chain with superantigen SEB. Bound: 1SBB. Unbound: 1BEC (RMSD: 0.50 Å) & 1SE4 (RMSD: 0.83 Å). D1 is the best prediction within the top 54000 rank, which has an iRMSD of 10.24 Å. D2 is a hit with an iRMSD: 2.13 Å found at the rank 81598. The unbound receptor and ligand complex are shown in green and pale blue while the predicted ligand is shown in magenta.