Table Info

Table 1.

List of data sources and tools useful in VS approaches applicable to COVID-19

Database and resources	Pre-treatment tools	Docking tools	MD tools	Analytics Platforms
DUD-E web server (useful docking decoys)	OpenBabel/Pybel (package for creating or converting different ligand/protein types)	PyRx (python package) for VS of libraries of compounds against potential drug targets	GROMACS	KNIME (broad range of free/commercial packages for analysis)
SWEETLEAD (database of curated chemicals)	ProTox (virtual lab for the prediction of toxicities of small molecules)	AutoDock Vina (C++/C)	AMBER, a suite of biomolecular simulation programs, (MM-PBSA and MM-GBSA for clusters/GPUs)	Molinspiration (broad range of cheminformatics software tools)
ChEMBL (curated database of bioactive molecules with drug-like properties)	LigandScout (generates 3D pharmacophore models for VS)	Autodock (C++/C)	SimpleRun (equilibrate protein-ligand complex and produce MD simulation)	PlayMolecule (one-clink molecular discovery)
SuperDRUG2 (resource for approved/marketed drugs)	PlayMolecule (preparation of protein for MD simulations)	rDock (ANSI C++)	Desmond from Schrödinger	ChemBioServer 2.0 (filtering, clustering, and VS)
DrugBank (information on drugs and drug targets)	LigPrep from Schrödinger	YASARA (AutoDock/Autodock Vina)	Schrodinger’s MD	Weka Software (Data mining: practical machine learning tools and techniques)
GenBank (NIH genetic sequence database)	MetaPocket: (improve protein ligand binding site prediction)	GOLD (genetic optimization for ligand docking)	YASARA (GROMACS module)	ChemoInfo (cheminformatic tools and databases for pharmacology)
LOPAC (library of pharmacologically active compounds)	Pockdrug server (druggability prediction)	MTiOpenScreen online webserver for VS	-	-
UniProt (database of FASTA protein sequences and functional information)	AMMOS2 web service (refinement of protein–small organic molecule complexes)	iDock (VS tool)	-	-
PubChem (large database of chemicals)	BindingDB (information on properties of ligands/targets)	FireDock (scoring of protein–protein docking solutions)	-	-
HOMSTRAD (HOMologous STRucture Alignment Database) is a curated database of structure-based alignments for homologous protein families	ReScore (+ scoring docked positions)	MVD	-	-
-	MedChemExpress (MCE) includes high quality inhibitors and recombinant proteins	-	-	-
-	ASINEX’s BioDesign (with key structural features of known pharmacologically relevant natural)	-	-	-
-	ACPYPE (or AnteChamber PYthon Parser interfacE), a ANTECHAMBER wrapper script for the generation of small molecule topologies and parameters	-	-	-

DUD-E: Directory of Useful Decoys-Enhanced; MM-PBSA: molecular mechanics Poisson-Boltzmann surface area; MVD: Molegro Virtual Docker; 3D: three-dimensional; -: blank cell

Declarations

Author contributions

BS: Conceptualization, Investigation, Writing—original draft, Writing—review & editing, Validation, Supervision.

Conflicts of interest

The author declares that he have no conflicts of interest.

Ethical approval

Not applicable.

Consent to participate

Not applicable.

Consent to publication

Not applicable.

Availability of data and materials

Not applicable.

Funding

Not applicable.

Copyright

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