Journal of Cheminformatics

Table 2 Adjusted Rand Indices, BEDROC, and AUCROC values.

From: Application of 3D Zernike descriptors to shape-based ligand similarity searching

Comparison Method
Descriptors	Metric	Order	Adjusted Rand Index	BEDROC (α = 160.9)	BEDROC (α = 32.2)	ROC AUC
3DZD	Correlation coefficient	4	0.299	0.506	0.453	0.694
		6	0.256	0.590	0.494	0.708
		8	0.422	0.739	0.654	0.738
		10	0.465	0.614	0.536	0.724
		12	0.487	0.697	0.630	0.732
		14	0.442	0.697	0.618	0.733
	Euclidean	4	0.278	0.338	0.329	0.680
		6	0.278	0.526	0.446	0.704
		8	0.357	0.678	0.621	0.738
		10	0.395	0.594	0.553	0.722
		12	0.487	0.658	0.610	0.730
		14	0.372	0.717	0.622	0.743
	Manhattan	4	0.270	0.318	0.329	0.686
		6	0.260	0.484	0.427	0.703
		8	0.328	0.698	0.619	0.732
		10	0.408	0.591	0.619	0.736
		12	0.393	0.637	0.591	0.732
		14	0.213	0.656	0.598	0.748
USR	Correlation coefficient	12	0.213	0.697	0.617	0.695
		16 (Kurtosis)	0.227	0.721	0.651	0.707
	Euclidean	12	0.270	0.760	0.639	0.708
		16	0.270	0.760	0.642	0.709
	Manhattan	12	0.343	0.762	0.661	0.718
		16	0.328	0.782	0.675	0.720
SIMCOMP	(Maximal Common Subgraph)	-	0.400	0.847	0.779	0.808
EVA	-	σ = 100 cm^-1	0.442	-	-	-
		σ = 50 cm^-1	0.388	-	-	-
		σ = 20 cm^-1	0.381	-	-	-
UNITY2D	-	-	0.247	-	-	-
MACCS	(Tanimoto)	166 bit key	0.364	0.778	0.659	0.742
MOLPRINT2D	(Tanimoto)		0.516	0.848	0.755	0.806
Atom Count	-		0.400	0.467	0.460	0.850

For the 3DZD, orders of expansion 4-14 have been applied and similarities calculated using the correlation coefficient, the Euclidean and the scaled Manhattan distances. For the USR the fourth statistical moment kurtosis has also been calculated. Hierarchical clustering was done using Ward's method. Results for the EVA and UNITY2D descriptors (for 7 clusters) have been taken from Table 2 in the article by Takane and Mitchell.

Back to article page

ISSN: 1758-2946

Contact us

Submission enquiries: journalsubmissions@springernature.com