MolScore: a scoring, evaluation and benchmarking framework for generative models in de novo drug design

Table 2 Functionality available within the molscore sub-package

			License key required	References
Scoring functions	Descriptors	RDKit Descriptors	No	[23]
		Linker Descriptors	No	[32]
		Penalised logP	No	[9]
		Maximum number of consecutive rotatable bonds	No
	Similarity	Isomer similarity	No	[8]
		Fingerprint similarity	No	[8]
		Molecular substructure match	No	[8, 19]
		Molecular substructure filters	No	[19]
		ROCS	Yes	[33]
		Open 3D Align	No	[34]
	Applicability domain	Maximum similarity	No	[35]
		Feature range	No	[35]
		Physchem range	No	[35]
	Predictive models	Scikit-learn models	No	[28]
		PIDGINv5	No	[30, 36]
		ChemProp	No	[27]
		ADMET-AI	No	[37]
	Docking	Glide	Yes	[38]
		PLANTS	Yes	[39]
		GOLD	Yes	[40]
		OEDock	Yes	[41]
		Smina	No	[42]
		Gnina	No	[43]
		Vina	No	[44]
		rDock	No	[45]
	Synthesizability	SA score	No	[46]
		RA Score	No	[25]
		AiZynthFinder	No	[26]
		Reaction filters	No	[47]
Scoring function utilities	Fingerprints	ECFP (Morgan), Atom-pair, Topological-torsions, MACCS keys, RDKit, Avalon, Pharm2D	No	[23]
	Similarity measure	Tanimoto, All bit, Asymmetric, Braun Blanquet, Cosine, McConnaughey, Dice, Kulczynski, Russel, On bit, Rogot Goldberg, Sokal	No	[23]
	Molecule preparation pipelines	GypsumDL	No	[48]
		Ligprep	Yes	[49]
		Epik	Yes	[50]
		Moka	Yes	[51]
Diversity filters		Unique	No
		Occurrence	No
		IdenticalMurckoScaffold	No	[52]
		IdenticalTopologicalScaffold	No	[52]
		CompoundSimilarity	No	[52]
		ScaffoldSimilarityAtomPair	No	[52]
		ScaffoldSimilarityECFP	No
Transformation functions		Normalise	No
		Linear threshold	No	[8]
		Gaussian threshold	No	[8]
		Step threshold	No
Aggregation functions		Weighted sum	No
		Auto-weighted sum	No	[53]
		Product	No
		Weighted Product	No
		Auto-weighted product	No	[53]
		Geometric Mean	No
		Arithmetic Mean	No
		Pareto front	No	[53]

ISSN: 1758-2946