Table 1.

Public databases, algorithms, and software related to TCM network pharmacology.

Type		Name	Description	Website for database or tool	Reference
Databases	TCM-related databases	TCM-Mesh	An integration of database and a data-mining system for network pharmacology analysis of TCM preparations	http://mesh.tcm.microbioinformatics.org	Zhang et al., 2017
		TCM database@Taiwan	The world’s largest and most comprehensive free small molecular database on TCM for virtual screening	http://tcm.cmu.edu.tw	Chen, 2011
		HIT	A comprehensive and fully curated database to complement available resources on protein targets for FDA-approved drugs as well as the promising precursor compounds	http://lifecenter.sgst.cn/hit	Ye et al., 2011
		TCMSP	A unique systems pharmacology platform of TCMs that captures the relationships among drugs, targets, and diseases	http://lsp.nwu.edu.cn/tcmsp.php	Ru et al., 2014
		TCMID	A comprehensive database that provides information and bridges the gap between TCM and modern life sciences	http://www.megabionet.org/tcmid	Xue et al., 2013
	Drug-related databases		A unique bioinformatics and cheminformatics resource that combines detailed drug data with comprehensive drug target information	https://www.drugbank.ca	Wishart et al., 2006
		STITCH	A database of known and predicted interactions between chemicals and proteins	http://stitch.embl.de	Kuhn et al., 2014
		ChEMBL	An Open Data database containing binding, functional, and ADMET information for a large number of drug-like bioactive compounds	https://www.ebi.ac.uk/chembl	Gaulton et al., 2012
		PubChem	A public information system for analyzing the bioactivities of small molecules	https://pubchem.ncbi.nlm.nih.gov	Wang et al., 2009
	Target-related databases	STRING	A database of known and predicted protein-protein interactions	https://string-db.org	Szklarczyk et al., 2015
		HPRD	An object database that integrates a wealth of information relevant to the function of human proteins in health and disease	http://www.hprd.org	Peri et al., 2003
		MINT	A database that focuses on experimentally verified protein-protein interactions mined from the scientific literature by expert curators	https://mint.bio.uniroma2.it	Zanzoni et al., 2002
		IntAct	A freely available, open-source database system and analysis tool for molecular interaction data	https://www.ebi.ac.uk/intact	Kerrien et al., 2012
		Reactome	A free, open-source, curated, and peer-reviewed pathway database	https://reactome.org	D’Eustachio, 2009
		HAPPI	An online database of comprehensive human annotated and predicted protein interactions	http://discovery.informatics.uab.edu/HAPPI	Chen et al., 2009
	Disease-related databases	OMIM	A comprehensive, authoritative compendium of human genes and genetic phenotypes that is freely available and updated daily	https://www.omim.org	Hamosh et al., 2002
		GAD	A database of genetic association data from complex diseases and disorders	https://geneticassociationdb.nih.gov	Becker et al., 2004
Algorithms		Random walk	An algorithm that predicts potential drug-target interactions on a large scale under the hypothesis that similar drugs often target similar target proteins and the framework of Random Walk	https://www.rdocumentation.org/packages/diffusr/versions/0.1.4/topics/random.walk	Chen et al., 2012
		PRINCE	A global, network-based method for prioritizing disease genes and inferring protein complex associations	https://github.com/fosterlab/PrInCE	Vanunu et al., 2010
Software		Cytoscape	A software environment for integrated models of biomolecular interaction networks	https://cytoscape.org	Shannon et al., 2003
		Pajek	A tool for complex network analysis	http://mrvar.fdv.uni-lj.si/pajek	Dohleman, 2006

These public databases are categorized into four types: TCM-related, drug-related, target-related, and disease-related. Publicly available tools and visualization software use data from these databases. Websites and references are provided for all of these resources.