Table 3:

Summary of the benchmark results reported in the literature. Results of the different methods tested on the same test set are grouped together for comparison. The first column “Test set” shows the number of test cases and the original references (shown in parentheses) reporting the test results. ^a Performance of affinity prediction is reported in terms of Pearson correlation coefficient, R². Correlation coefficient is calculated between experimental binding affinities and predicted binding affinities. Benchmarks without affinity prediction are shown as dashes. ^b Performance of pose identification is reported as success rate. The criteria for a correct prediction is shown in the (rank, RMSD) format. For example, (1, 2.5Å) means the top-1 prediction that has RMSD less than 2.5 Å to the native pose. Benchmarks without pose identification are shown as dashes. ^c RLDOCK, rDock, rDock_solv, AutoDock Vina use 38 instead of 42 complexes. MORDOR uses 32 instead of 42 complexes. ^d Only several top performing models evaluated in literature (57) are listed for this benchmark dataset. ^e Three outliers 3GX3, 2ESI and 1F1T are excluded in the binding affinity calculation. ^f Near native poses are sampled through rDock reference ligand method (67) and ^g Average and standard deviation from 100 sets of 100 random docking poses out of a pool of 1000 decoy conformations. ^h Native pose is included in pose identification. are included in pose identification. ⁱ RNA-adapted AutoDock scoring function (137) is used. ^j Scoring function is used to guide the docking instead of using default Vina scoring function.

Test set	Scoring function	Docking engine	Affinitya prediction(R2)	Poseb identification(%)
42 (70; 71; 142; 175) complexes			Correlation	(1, 2.0Å)	(3, 2.0Å)
	RLDOCK	RLDOCK	-	55.3c	60.5c
	ITScore-NL	DOCK6	-	50.0	54.7
	LigandRNA+DOCK6	DOCK6	-	47.6	54.8
	rDock_solv	rDock 2014	-	39.5c	55.3c
	DOCK6	DOCK6	-	35.7	45.2
	LigandRNA	DOCK6	-	35.7	42.9
	AutoDock Vina	AutoDock Vina	-	31.6c	44.7c
	DrugScoreRNA	DOCK6	-	31.0	42.9
	rDock	rDock 2014	-	28.9c	47.4c
	MORDOR	MORDOR	-	-	62.5c
34 (57; 142; 176) complexesd			Correlatione	(3, 1.5Å)	(5, 3.0Å
	SPA-LN	rDock 2014	0.36	50.6	76.6
	Gold Fitness	GOLD5.0.1	0.25	42.9	73.2
	ASP	GOLD5.0.1	0.29	42.9	66.1
	rDock_solv	rDock 2006.2	0.18	41.1	73.2
	rDock	rDock 2006.2	0.15	33.9	60.7
	ITScore-NL	-	0.41	-	-
56 (67; 141; 176) complexes			Correlation	-	(1, 2.5Å)
	RNAPosers	rDock 2014	-	-	62.5f
	rDock_solv	rDock 2014	-	-	54±3g
	SPA-LN	rDock 2014	-	-	54±3g,h
	AutoDock Vina	AutoDock Vina	-	-	29±2g
	GlideScore	Glide (v.57111)	-	-	17.8
31 (137; 141; 173)			Correlation	(1, 2.0Å)	(1, 2.5Å)
	RNAPosers	rDock 2014	-	57.1f	61.9f
	DrugScoreRNA	AutoDock 3.0.5j	-	41.9	45.2
	AutoDocki	AutoDock 3.0.5j	-	25.8	35.5
77 (142; 176; 235) complexes			Correlation	(3, 1.5Å)	(5, 3.0Å)
	ITScore-NL	AutoDock 4.2	0.41	71.4h	90.9h
	SPA-LN	rDock 2014	0.33	50.6h	76.6h