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Table 1 Chemical similarity methods evaluated in this study

From: Comparative analysis of chemical similarity methods for modular natural products with a hypothetical structure enumeration algorithm

Method

Type

ECFP0

Circular fingerprint

ECFP2

Circular fingerprint

ECFP4

Circular fingerprint

ECFP6

Circular fingerprint

FCFP0

Circular fingerprint

FCFP2

Circular fingerprint

FCFP4

Circular fingerprint

FCFP6

Circular fingerprint

MACCS

Substructure keys-based fingerprint

PubChem

Substructure keys-based fingerprint

E-State

Substructure keys-based fingerprint

Klekota–Roth

Substructure keys-based fingerprint

CDK (default)

Topological fingerprint

CDK (extended)

Topological fingerprint

CDK (hybridization)

Topological fingerprint

CDK (graph-only)

Topological fingerprint

LINGO

Lexicographic fingerprint

GRAPE/GARLIC

Retrobiosynthesis and alignment