Figure 9.

Examples of docking prediction. The best prediction within 50 ranks by PI-LZerD-2, the base LZerD, and naive post-filtering is shown in green, yellow, and red, respectively. The correct docking pose is shown in blue. Receptor proteins are shown in gray. First, predictions using 10 residue-shifted PPI site information are shown for A, 1BUH; B, 1MLC. For 1BUH, the iRMSD (Å) of prediction by PI-LZerD-2/post-filtering/base LZerD was 1.03/9.09/9.91. The rank of the decoys was 8/24/17. The sensitivity (= specificity, since the size of the shifted PPIs are same as the correct PPI) of the shifted PPI region was 0.33 for 1BUHA and 0.44 for 1BUHB. For 1MLC, iRMSD (Å) and the rank of the best prediction within 50 ranks by PI-LZerD-2/post-filtering/base LZerD were 0.89 Å (34)/8.37 Å (9)/14.35 Å (22). The ranks are shown in the parentheses. The sensitivity (= specificity) of the shifted PPI region was 0.55 for chain A and B, and 0.44 for chain E. C and D are predictions using actual PPI site predictions by meta-PPPISP for proteins from the iPFAM dataset. C, 1ADU. The iRMSD (Å) and the rank of the predictions by PI-LZerD-2/post-filtering/base LZerD were 1.04 Å (48)/14.90 Å (37)/10.85 Å (43). The sensitivity/specificity of PPI site predictions were 0.77/0.47 for 1ADUA, and 0.00/0.00 for 1ADUB. D, 1BMT. The iRMSD (Å) and the rank of the predictions by PI-LZerD-2/post-filtering/base LZerD were 2.31 Å (36)/14.44 Å (31)/13.02 Å (44). The sensitivity/specificity of PPI site predictions were 0.11/0.06 for 1BMTA, and 0.22/0.11 for 1BMTB. The last two examples are unbound docking cases with actual PPI predictions by meta-PPISP. E, 1OPH. The iRMSD (Å) and the rank of the predictions by PI-LZerD-2/post-filtering/base LZerD were 3.76 Å (42)/5.71 Å (39)/10.28 Å (16). The sensitivity/specificity of PPI site predictions were 1.00/0.32 for 1OPHA, and 0.70/0.18 for 1OPHB. F, 1IQD. The PI-LZerD-2/post-filtering/base LZerD: 2.91 Å (23)/6.97 Å (16)/12.80 Å (32). The sensitivity/specificity of PPI site predictions were 0.53/0.16 for 1IQDA, and 0.89/0.20 for 1IQDB.

Li and Kihara BMC Bioinformatics 2012 13:7   doi:10.1186/1471-2105-13-7
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