Table 7.

Correlation evaluation of the PHOENIX scoring function compared to other commonly used scoring functions on three subsets (HIV-1 Protease, Trypsin, Carbonic Anhydrase II) of the PDBbind 2002 set. Correlation statistics presented are the number of complexes tested (N), Pearson correlation coefficient (R_p), standard deviation (SD), mean error (ME), Spearmen correlation coefficient (R_s). Results from the commonly used scoring functions taken from the Wang et al. study²⁶ are presented for comparison purposes.

	HIV-1 Protease					Trypsin					Carbonic Anhydrase II
Scoring Function	N	Rp	SD	ME	Rs	N	Rp	SD	ME	Rs	N	Rp	SD	ME	Rs
	8		1.6	1.3		4		1.9	1.3		3		3.2	2.9
PHOENIX	2	0.563	5	5	0.434	0	0.476	0	8	0.574	9	0.539	6	7	0.444
	7					4					3
SFSscore::met	4	0.361	na	na	0.312	0	0.853	na	na	0.848	7	0.717	na	na	0.485
	8		1.2	1.0		4		1.1	0.8		3		1.1	0.8
X-Score::HPScore	2	0.429	5	1	0.436	5	0.754	5	8	0.725	9	0.544	8	5	0.547
	8		1.2	1.0		4		0.9	0.7		3		1.2	0.9
X-Score::HMScore	2	0.379	8	4	0.334	5	0.823	9	5	0.824	9	0.495	3	5	0.341
	8		1.2	1.0		4		1.1	0.9		3		1.2	0.9
X-Score::HSScore	2	0.400	7	5	0.322	5	0.753	5	1	0.766	9	0.417	8	1	0.448
	8		1.2	1.0		4		1.0	0.8		3		1.1	0.8
DrugScore::Pair	2	0.377	8	4	0.315	5	0.780	9	2	0.818	9	0.622	0	3	0.501
	8		1.2	1.0		4		1.2	0.9		3		1.2	0.9
DrugScore::Surf	2	0.401	7	2	0.317	5	0.674	9	9	0.753	9	0.512	1	7	0.269
	8		1.2	1.0		4		1.0	0.8		3		1.1	0.8
DrugScore::Pair/Surf	2	0.384	8	4	0.322	5	0.780	9	2	0.807	9	0.623	0	3	0.495
	8		1.3	1.0		4		1.3	0.9		3		1.1	0.8
Sybyl::D-Score	2	0.342	0	3	0.305	5	0.617	7	8	0.736	9	0.584	4	6	0.441
	8		1.3	1.0		3		1.0	0.8		3		1.0	0.8
Sybyl::PMF-Score	2	0.246	4	9	0.226	7	0.513	2	6	0.523	9	0.655	7	0	0.652
	8		1.3	1.0		4		1.4	1.0		3		1.0	0.7
Sybyl::G-Score	2	0.350	0	5	0.335	5	0.580	2	6	0.728	9	0.643	8	9	0.649
	8		1.2	1.0		4		1.1	0.9		3		1.1	0.7
Sybyl::ChemScore	2	0.376	8	5	0.350	5	0.761	3	1	0.749	9	0.609	2	6	0.663
	8		1.3	1.0		4		1.3	1.0		3		1.1	0.8
Sybyl::F-Score	0	0.361	1	8	0.375	5	0.663	1	5	0.610	5	0.371	5	7	0.145
	8		1.1	0.9		4		1.5	1.2		1		1.7	1.3
Cerius2::LigScore	1	0.528	8	9	0.496	0	0.392	9	7	0.467	8	0.154	8	4	−0.323
	8		1.2	1.0		4		1.1	0.8		3		0.9	0.7
Cerius2::PLP1	2	0.458	3	2	0.395	5	0.729	9	8	0.785	9	0.718	8	6	0.606
	8		1.2	1.0		4		1.1	0.8		3		0.9	0.6
Cerius2::PLP2	2	0.438	5	3	0.414	5	0.754	5	4	0.802	9	0.735	6	7	0.781
	8		1.2	1.0		4		1.0	0.8		3		1.1	0.8
Cerius2::PMF	2	0.411	6	3	0.342	3	0.775	6	5	0.740	9	0.604	2	7	0.603
	8		1.3	1.1		4		1.2	1.0		3		1.2	0.8
Cerius2::LUDI1	2	0.208	5	1	0.123	5	0.670	9	1	0.698	8	0.065	1	6	0.335
	8		1.3	1.1		4		1.2	0.9		3		1.2	0.8
Cerius2::LUDI2	2	0.274	3	1	0.181	5	0.696	5	5	0.725	9	0.470	5	9	0.519
	8		1.3	1.1		4		1.2	1.0		3		1.2	0.9
Cerius2::LUDI3	2	0.248	4	0	0.174	5	0.679	8	0	0.690	9	0.433	7	1	0.554
	6		1.2	1.0		3		1.6	1.3		3		1.2	0.9
GOLD::GoldScore	9	0.386	5	0	0.391	6	0.029	5	2	−0.012	4	0.539	5	0	0.420
	7		11	0.9		4		1.4	1.1		3		1.1	0.8
GOLD::GoldScore_opt	8	0.555	3	2	0.579	2	0.590	1	4	0.673	7	0.585	7	6	0.532
	7		1.1	0.9		4		1.6	1.3		3		1.2	0.8
GOLD::ChemScore	8	0.404	9	8	0.386	4	0.388	1	3	0.348	9	0.498	2	9	0.307
	8		1.2	1.0		4		1.4	1.2		3		1.0	0.8
GOLD::ChemScore_opt	0	0.429	4	2	0.393	4	0.520	9	1	0.565	9	0.639	8	0	0.454
	8		1.3	1.0		4		1.7	1.3		3		1.1	0.7
HINT	2	0.313	2	4	0.264	5	0.135	3	7	0.251	9	0.599	3	8	0.689