Modern drug discovery for inflammatory bowel disease: The role of computational methods

Table 2 Bioinformatics resources for the identification of drug targets

Tool/Database	Description
Open Targets Platform	To facilitate systematic target identification and prioritization for drug discovery based on underlying evidence, the Open Targets Platform offers users a searchable knowledgebase and user interface[123]
SELF-BLM	A self-training support vector machine-based bipartite local model that predicts drug-target interactions[136]
iDTIESBoost	A model for detecting drug-target interactions based on evolutionary and structural features[137]
GEO	Database that stores array- and sequence-based transcriptomics data that can be applied to functional genomics[138]
DASPfind	Predicts drug-target protein interactions that stem from shared structural features[139]
NetCBP	Network methods for predicting drug-target interactions. Furthermore, it suggests new drugs even when no data on their interactions with their targets are available[140]
DbMDR	Offers a database of multidrug resistance (MDR) genes and their orthologs, which could be used to develop new treatments[141]
TDR targets	Drug development molecular target identification and prioritization[142]
DrugBank	An extensive drug database with annotations covering drug targets and mechanisms of action[143]
PDTD	Database of potential proteins for in silico drug target identification[144]
DEG	Contains all known essential genes from different organisms[145]
TTD	Publicly accessible cross-links database that provides inclusive information about known therapeutic targets with related information, i.e. pathway information and the corresponding drugs/ligands[146]
KEGG	Offers information about the pathway, gene and ligands in three different databases, i.e. Pathway, Gene and Ligand[147]
Genecards	Officially known as Genecards: The Human Gene Database, it is an all-inclusive, authoritative compilation of annotative information about human genes[148]
DisGeNET	A public resource that houses a massive database of genetic variants and their links to human disease[149]
CTD	The Comparative Toxicogenomics Database is a vast, freely accessible database with the objective of increasing understanding of the effects of environmental exposures on human health. It includes information on chemical-gene/protein interactions, chemical-disease relationships and gene-disease links that has been curated by humans[150]
UniProt	The Universal Protein Resource is the world’s most comprehensive, high-quality and freely accessible database of protein sequence and functional information[151]

SELF-BLM: Self-training bipartite local model; GEO: Gene Expression Omnibus; UniProt: Universal Protein Resource; CTD: Comparative Toxicogenomics Database; KEGG: Kyoto Encyclopedia of Genes and Genomes; TTD: Therapeutic Target Database; DEG: Database of Essential Genes; PDTD: Potential Drug Target Database; DbMDR: Database of multidrug resistance: NetCBP: Network-Consistency-based Prediction.