Table 2.

Pairwise comparison of scoring methods surflex-dock (surf), ICM, and their consensus (maxz), at three testing fractions decided a priori. For each pair of scoring methods, differences and standard errors of estimated hit enrichment curves are shown, along with raw and Benjamini-Hochberg adjusted p-values

	N tested = 3 $(r=0.001)$				N tested = 32 $(r=0.01)$				N tested = 321 $(r=0.1)$
	Diff	Std Err	Raw p	Adj p	Diff	Std Err	Raw p	Adj p	Diff	Std Err	Raw p	Adj p
EmProc
maxz - surf	0.0000	0.0005	1.000	1.000	− 0.0118	0.0237	0.6200	0.6970	0.0588	0.0254	2.07e−02	6.21e−02
maxz - icm	0.0118	0.0143	0.410	0.527	0.0824	0.0402	0.0407	0.0733	0.3060	0.0541	1.60e−08	1.44e−07
surf - icm	0.0118	0.0142	0.409	0.527	0.0941	0.0429	0.0281	0.0632	0.2470	0.0626	7.91e−05	3.56e−04
McNemar
maxz - surf	0.0000	0.0000	1.000	1.000	− 0.0118	0.0311	0.705	0.794	0.0588	0.0255	2.53e−02	7.60e−02
maxz - icm	0.0118	0.0203	0.564	0.725	0.0824	0.0557	0.144	0.260	0.3060	0.0552	2.07e−06	1.86e−05
surf - icm	0.0118	0.0203	0.564	0.725	0.0941	0.0614	0.131	0.260	0.2470	0.0642	3.86e−04	1.74e−03
IndJZ
maxz - surf	0.0000	0.0138	1.000	1.000	− 0.0118	0.0497	0.8130	0.915	0.0588	0.0609	3.34e−01	5.28e−01
maxz - icm	0.0118	0.0143	0.411	0.528	0.0824	0.0482	0.0874	0.197	0.3060	0.0668	4.74e−06	4.26e−05
surf - icm	0.0118	0.0143	0.409	0.528	0.0941	0.0471	0.0458	0.137	0.2470	0.0693	3.63e−04	1.64e−03
CorrBinom
maxz - surf	0.0000	0.0000	1.000	1.000	− 0.0118	0.0311	0.705	0.793	0.0588	0.0255	2.12e−02	6.35e−02
maxz - icm	0.0118	0.0203	0.563	0.724	0.0824	0.0557	0.139	0.251	0.3060	0.0552	3.07e−08	2.76e−07
surf - icm	0.0118	0.0203	0.563	0.724	0.0941	0.0614	0.125	0.251	0.2470	0.0642	1.20e−04	5.40e−04