Effectiveness of molecular fingerprints for exploring the chemical space of natural products

Table 3 List of molecular fingerprints evaluated in this study, detailing for each the original publication year, the algorithm category, bit information type, number of bits, source package and parameters used for the calculation

Name	Year	Category	Type	Size	Source	Parameters
Topological Torsion (TT) [28]	1987	Path	Count	4096	RDKIT [14]	targetSize = 4
Atom Pair (AP) [29]	1985	Path	Count	4096	RDKIT [14]	N.A
Avalon [30]	2006	Path	Count	1024	RDKIT [14]	N.A
Daylight [31]	1973	Path	Binary	1024	CDK [15]	Depth = 7
Depth First Search (DFS) [32]	2005	Path	Binary	4096	jCompoundMapper [16]	Depth = 7
All Shortest Paths (ASP) [16]	2011	Path	Binary	4096	jCompoundMapper [16]	Depth = 7
RDKIT [14]	2012	Path	Binary	2048	RDKIT [14]	Depth = 7
Pharmacophore Pairs (PH2) [33]	2006	Pharmacophore	Binary	4096	jCompoundMapper [16]	N.A
Pharmacophore Triplets (PH3) [33]	2006	Pharmacophore	Binary	4096	jCompoundMapper [16]	N.A
MACCS [34]	2002	Substructure	Binary	166	RDKIT [14]	N.A
PubChem [35]	2009	Substructure	Binary	881	CDK [15]	N.A
ESTATE [36]	1995	Substructure	Binary	79	CDK [15]	N.A
Klekota-Roth (KR) [37]	2008	Substructure	Binary	4860	CDK [15]	N.A
Extended Connectivity (ECFP) [38]	2010	Circular	Binary	1024	RDKIT [14]	Radius = 2
Functional Class (FCFP) [38]	2010	Circular	Binary	1024	RDKIT [14]	Radius = 2
RAD2D [39]	2004	Circular	Binary	4096	jCompoundMapper [16]	N.A
LSTAR [16]	2011	Circular	Binary	4096	jCompoundMapper [16]	N.A
LINGO [40]	2005	String	Binary	1024	CDK [15]	N.A
MinHashed (MHFP) [18]	2018	String	Categorical	1024	Ref. [19]	Radius = 3
MinHashed Atom Pair (MAP4)¹⁷	2020	String	Categorical	1024	Ref. [18]	Radius = 2

ISSN: 1758-2946