An Updated Review of Computer-Aided Drug Design and Its Application to COVID-19

Table 3

A list of pharmacophore modelling tools.

Tools	Description	Reference
Catalyst	Catalyst program is based on an algorithm that identifies three-dimensional configurations of chemical features common to a set of ligands, wherein each configuration is scored based both on estimated rarity and the level to which it is common to the input set.	[83]
LigandScout	LigandScout is a fully automated tool for generating pharmacophore models which detect and classifies protein-ligand interactions (hydrogen bond interactions, charge transfers, and lipophilic regions) which form the basis of the pharmacophore model used for high throughput virtual screening.	[84]
DISCO	DISCO is an automated pharmacophore method which examines the data to find all pharmacophore hypothesis that fit and serves as a complement to 3D QSAR.	[85]
PharmaGist	PharmaGist is a freely available web server used for generating ligand-based pharmacophore models, wherein the input is a set of drug-like molecules (maximum limit of 32 drug-like molecules) that have a binding affinity to the target protein.	[86]
PharmMapper	PharmMapper server is a freely available web server that is commonly used for the identification of potential target receptors for a given small molecule using the pharmacophore mapping approach.	[87]
Pharmer	Pharmer is a pharmacophore search program that organizes molecular data using the Pharmer KDB-tree and bloom fingerprints which allow rapid screening of millions of molecules in a reasonable time.	[88]
PHASE	PHASE is an advanced pharmacophore-based tool that comprehensively maps the common spatial arrangement of functional groups in a set of bioactive ligands using a novel tree-based partitioning algorithm.	[89]
ZINCPharmer	ZINCPharmer is an online web server for the screening of small molecules from the ZINC database using the Pharmer pharmacophore search program. An initial pharmacophore hypothesis can be derived either from PDB structures or by importing pharmacophore models developed using other third-party tools.	[90]
e-Pharmacophore	The e-pharmacophore method generates energetically optimized, structure-based pharmacophore models which can be used for screening of millions of compounds. The method uses the glide XP scoring function to score protein-ligand interactions and has good database screening enrichments.	https://www.schrodinger.com/e-pharmacophores
GASP	GASP program uses a genetic algorithm (GA) for the superimposition of a set of flexible ligands where the ligand possessing the lowest number of chemical features are chosen as a template, onto which other molecules are fitted.	[91]
Shape4	Shape4 is a structure-based pharmacophore program developed is to enhance increase the efficiency of database searching by considering the topographical constraints of the target binding site and consequently helps to help minimize the false positive rate.	[92]
Snooker	Snooker is a structure-based pharmacophore tool that generates pharmacophore hypotheses from homology models with critical residues for ligand binding identified through the study of Shannon entropies of structurally conserved positions in multiple sequence alignments and does not rely on the prior information of ligand structure or interactions.	[93]
Pocketv.2	Pocket v.2 is an automated program to generate a pharmacophore model from a given protein−ligand complex structure and has been designed using the pocket module of LigBuilder.	[94]
GALAHAD	GALAHAD is a pharmacophore program developed to perform flexible alignment of small molecules that bind to a target protein and share similar interaction patterns and shapes.	[95]