Table 5.

Correlation evaluation of the PHOENIX scoring function compared to other commonly used scoring functions on the PDBbind v2002 set. Correlation statistics presented are the number of complexes tested (N), Pearson correlation coefficient (R_p), standard deviation (SD), mean error (ME), slope (a) in the linear regression (y = ax + b), and intercept (b). Results from the commonly used scoring functions taken from the Wang et al. study²⁶ are presented for comparison purposes.

Scoring Function	N	Rp	SD	ME	a	b
PHOENIX	796	0.524	1.98	1.56	0.37	4.27
SFCscore::met	800	0.585	1.8	1.37	0.82	1.23
X-Score::HPScore	800	0.514	1.89	1.47	0.71	2.03
X-Score::HMScore	800	0.566	1.82	1.42	0.92	1.18
X-Score::HSScore	800	0.506	1.9	1.48	0.93	1.24
DrugScore::Pair	800	0.473	1.94	1.51	4.90E-06	4.1
DrugScore::Surf	800	0.463	1.95	1.53	7.20E-05	4.48
DrugScore::Pair/Surf	800	0.476	1.94	1.5	4.70E-06	4.09
Sybyl::D-Score	800	0.322	2.09	1.67	9.70E-03	5
Sybyl::PMF-Score	785	0.147	2.16	1.74	6.43E-03	5.92
Sybyl::G-Score	800	0.443	1.98	1.56	9.13E-03	4.34
Sybyl::ChemScore	797	0.499	1.91	1.5	9.10E-02	3.9
Sybyl::F-Score	732	0.141	2.19	1.77	2.10E-02	6.06
Cerius2::LigScore	717	0.406	2	1.57	0.79	4.63
Cerius2::PLP1	800	0.458	1.96	1.52	2.30E-02	4.09
Cerius2::PLP2	800	0.455	1.96	1.53	2.60E-02	3.93
Cerius2::PMF	795	0.253	2.13	1.71	1.10E-02	5.37
Cerius2::LUDI1	790	0.334	2.08	1.66	2.60E-03	4.88
Cerius2::LUDI2	799	0.379	2.04	1.62	4.20E-03	4.28
Cerius2::LUDI3	800	0.331	2.08	1.67	3.20E-03	4.68
GOLD::GoldScore	694	0.285	2.16	1.72	2.40E-02	5.33
GOLD::GoldScore_opt	772	0.365	2.06	1.63	3.00E-02	4.7
GOLD::ChemScore	741	0.423	2	1.56	8.50E-02	4.65
GOLD::ChemScore_opt	762	0.449	1.96	1.52	8.60E-02	4.41
HINT	800	0.33	2.08	1.65	0.2	6.36