Table 2.

Selection of pseudoquery methods categorized by the underlying protein-interaction model.

Model	Methods	Description
Interaction fingerprint-based	SIFt [132]	Fingerprint encoding seven predefined types of target–ligand interactions.
	PLIP [133]	A web service for the detection and visualization of seven protein–ligand interaction types considering a 3D space.
	FLIP [134]	For each residue, 7 different interactions are represented in 10 bits.
	PADIF [135]	Fingerprints with the inclusion of information relative to the strength of interactions and unfavorable ones.
Pharmacophore-based	LigandScout [125]	Pharmacophores derived from six types of nonbonded protein-ligand interactions and volume constraints.
	FLAP [126]	Four-point pharmacophore fingerprints with a shape component.
	IChem [136]	Converts the protein–ligand interaction pattern in fingerprints and graphs.
	TIFP [137]	Encodes a string of unique triplets (two interacting atoms and an interaction pseudo-atom).