Table 5

The customized functions of all 29 databases discussed in this study and their representative applications. These functions fall into three classes: facilitating the rational use of drugs, discovering the potential therapeutic targets, and developing the new strategy for disease treatment

Class of Function	Customized Function of Each Analyzed Database	Typical Database(s)	Representative Applications of These Databases
Discovering the Potential Therapeutic Targets	Structure-based Drug Design or Identification	PDB PPTdb MemProt MD	PDB database was used to identify a novel AQP4 inhibitor binding deep inside this transporter based on the molecular dynamics using a high-resolution crystal AQP4 structure (Yu et al., 2016).
	Sequence-based Discovery of Target Druggability	TransportDB TTD TCDB	TransportDB database was adopted for predicting transporters from the genome and providing a breakthrough for the functional annotation of a large number of transporters (Frioux et al., 2020).
	Disease-specific Differential Expression Analysis	Human Protein Atlas EBI Expression Atlas VARIDT	Human Protein Atlas was used to extract the expression pattern of SLC16A1 and SLC16A3 for their clinical potential applications in the treatment of pancreatic adenocarcinoma (Yu et al., 2020).
	Structure Similarity Search by Transported Drugs	ChEMBL TTD DrugBank	ChEMBL database was used to identify a new inhibitor of serotonin transporter with comparable affinity to the commercial drug by structure similarity search and virtual screening (Sakai et al., 2021).
Developing the New Strategy for Disease Treatment	Interplay Analysis among Multiple DT Variabilities	VARIDT	VARIDT database was used to facilitate the interplay analysis of OAT2 in hepatocellular carcinoma between its disease-specific differential expression and histone acetylation (Wang et al., 2021).
	Functional Analysis Based on Signaling Pathways	KEGG PharmGKB	KEGG database was applied to identify the key transporter pathways involving in the development of breast cancer (Sakil et al., 2017) and the microgravity effects in epidermal stem cells (Li et al., 2020a).
	Functional Annotation and Systematic Classification	TCDB	TCDB database was adopted to facilitate the functional annotation and systematic classification of DT using its transporter automatic annotation pipeline (Graf et al., 2021; Peng et al., 2021).
Facilitating the Rational Use of Drugs	Prediction of DT-based Potential DDI	Transformer UCSF-FDA TransPortal PharmGKB	Transformer database was adopted to predict the potential DDIs for reducing the costs in novel drug development and optimizing the process of rational drug design (Carrascal-Laso et al., 2020)
	Drug Safety Assessment and Toxicity Prediction	Human Protein Atlas VARIDT EBI Expression Atlas	VARIDT was applied to reveal the biologic mechanism of bile acids efflux using the tissue-specific expression of two subunits of organic solute transporter in ileum (Zhou et al., 2020).
	Identification of Potential Drug Resistance	PharmGKB OMIM iMusta4SLC	PharmGKB database was used to predict the response of drugs in cancer treatment based on the pharmacogenomic analysis focusing on ATP binding cassette transporters (Hlaváč et al., 2020).