Enhance the performance of current scoring functions with the aid of 3D protein-ligand interaction fingerprints

BMC Bioinformatics

Table 2 Statistical results of the four selected scoring functions in the in situ scoring test

Data sets	X-Score			ChemPLP			ASP			GoldScore
Data sets	R ^a	SD ^b	k ^c	R	SD	k	R	SD	k	R	SD	k
The PDBbind refined set (N = 3446)	0.55	1.68	0.94	0.39	1.85	0.025	0.35	1.88	0.043	0.19	1.97	0.008
The PDBbind refined set (N = 2859)^d	0.52	1.65	0.97	0.41	1.76	0.027	0.34	1.81	0.040	0.17	1.90	0.007
HIV-1 protease (N = 303)	0.08	1.71	---	0.01	1.73	---	−0.09	1.77	---	−0.01	1.67	---
Carbonic anhydrase 2 (N = 230)	0.35	1.45	---	0.40	1.43	---	0.45	1.39	---	0.37	1.45	---
Beta-secretase 1 (N = 223)	0.73	1.07	---	0.65	1.18	---	0.70	1.15	---	0.58	1.29	---
Beta-Trypsin (N = 196)	0.75	1.34	---	0.55	1.52	---	0.61	1.50	---	0.43	1.63	---
Checkpoint kinase 1 (N = 61)	0.63	1.23	---	0.75	1.25	---	0.81	1.28	---	0.55	1.43	---

^aPearson correlation coefficient between the experimental binding constants and the binding scores produced by a scoring function
^bStandard deviation in regression (in logK _a units)
^cSlope of the regression line, which a parameter required in Eq. 4 for KGS2 to compute adjusted binding scores
^dThis set of results were particularly derived for Variation Model 1 (see the descriptions in Preparation of the reference library)

ISSN: 1471-2105