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Table 4 Common druggable targets/protein databases overview

From: In silico approach in reveal traditional medicine plants pharmacological material basis

Databases Developers Websites Abstract References
Binding DB Skaggs School of Pharmacy & Pharmaceutical Sciences, USA BindingDB is a public, web-accessible database of measured binding affinities, focusing chiefly on the interactions of proteins considered to be candidate drug-targets with ligands that are small, drug-like molecules [68]
BioGRID (Biological General Repository for Interaction Datasets) BioGRID, Canada BioGRID is an interaction repository with data compiled through comprehensive curation efforts. Our current index is version 3.4.151 and searches 63,354 publications for 1,493,749 protein and genetic interactions, 27,785 chemical associations and 38,559 post translational modifications from major model organism species. All data are freely provided via our search index and available for download in standardized formats [69]
DAVID (Database for Annotation, Visualization, and Integrated Discovery) Laboratory of Human Retrovirology and Immunoinformatics, USA The database for annotation, visualization and integrated discovery
Able to perform: Identify enriched biological themes, discover enriched functional-related gene groups, list interacting proteins and other functions
DRUGBANK Canadian Institutes of Health Research, Canada The DrugBank database is a unique bioinformatics and cheminformatics resource that combines detailed drug data with comprehensive drug target information. The database contains 9591 drug entries including 2037 FDA-approved small molecule drugs, 241 FDA-approved biotech drugs, 96 nutraceuticals and over 6000 experimental drugs. Additionally, 4661 non-redundant protein (sequences are linked to these drug entries [71]
GeneMANIA University of Toronto, Canada GeneMANIA finds other genes that are related to a set of input genes, using a very large set of functional association data. Association data include protein and genetic interactions, pathways, co-expression, co-localization and protein domain similarity. You can use GeneMANIA to find new members of a pathway or complex, find additional genes you may have missed in your screen or find new genes with a specific function, such as protein kinases. Your question is defined by the set of genes you input [72]
HPRD (Human Protein Reference Database) Johns Hopkins University and the Institute of Bioinformatics, USA HPRD is a database of curated proteomic information pertaining to human proteins. All the information in HPRD has been manually extracted from the literature by expert biologists who read, interpret and analyze the published data [73]
IntAct European Molecular Biology Laboratory IntAct is an open-source, open data molecular interaction database populated by data either curated from the literature or from direct data depositions [74]
KEGG (Kyoto Encyclopedia of Genes and Genomes) Kyoto University, Japan KEGG (Kyoto Encyclopedia of Genes and Genomes) is a database resource that integrates genomic, chemical and systemic functional information. In particular, gene catalogs from completely sequenced genomes are linked to higher-level systemic functions of the cell, the organism and the ecosystem. KEGG is widely used as a reference knowledge base for integration and interpretation of large-scale datasets generated by genome sequencing and other high-throughput experimental technologies. In addition to maintaining the aspects to support basic research, KEGG is being expanded towards more practical applications integrating human diseases, drugs and other health-related substances [75]
MAS3.0 CapitalBio, China MAS (Molecule Annotation System) is a whole data-mining and function annotation solution to extract and analyze biological molecules relationships from public knowledgebase of biological molecules and signification. MAS analysis platform is a web client program for interactive navigation in the knowledge base. MAS uses relational database of biological networks created from millions of individually modeled relationships between genes, proteins, diseases and tissues. MAS allow a view on your data, integrated in biological networks according to different biological context. This unique feature results from multiple lines of evidence which are integrated in MAS’ database. MAS Help to understand relationship of gene expression data [76]
MINT (The Molecular INTeraction Database) Department of Biology, University of Rome, Italy The MINT is a public repository for protein–protein interactions (PPI) reported in peer-reviewed journals. The database grows steadily over the years and at September 2011 contains approximately 235 000 binary interactions captured from over 4750 publications [77]
PharmMapper Server Shanghai Institute of Materia Medica, China PharmMapper Server is a freely accessed web-server designed to identify potential target candidates for the given probe small molecules (drugs, natural products, or other newly discovered compounds with binding targets unidentified) using pharmacophore mapping approach. Benefited from the highly efficient and robust mapping method, PharmMapper bears high throughput ability and can identify the potential target candidates from the database within a few hours [78]
Potential Drug Target Database (PDTD) Shanghai Institute of Materia Medica, China PDTD is a dual function database that associates an informatics database to a structural database of known and potential drug targets. PDTD is a comprehensive, web-accessible database of drug targets, and focuses on those drug targets with known 3D-structures. PDTD contains 1207 entries covering 841 known and potential drug targets with structures from the Protein Data Bank [79]
RCSB PDB (Protein Data Bank) Research Collaboratory for Structural Bioinformatics: Rutgers and UCSD/SDSC A global resource for the advancement of research and education in biology and medicine. Along with our Worldwide PDB collaborators, RCSB PDB curates, annotates, and makes publicly available the PDB data deposited by scientists around the globe. The RCSB PDB then provides a window to these data through a rich online resource with powerful searching, reporting, and visualization tools for researchers [80]
Reactome European Bioinformatics Institute (EMBL-EBI) The Reactome provides molecular details of signal transduction, transport, DNA replication, metabolism and other cellular processes as an ordered network of molecular transformations—an extended version of a classic metabolic map, in a single consistent data model [81]
STITCH (search tool for interactions of chemicals) European Molecular Biology Laboratory, Germany STITCH is a database of known and predicted interactions between chemicals and proteins. The interactions include direct (physical) and indirect (functional) associations; they stem from computational prediction, from knowledge transfer between organisms, and from interactions aggregated from other (primary) databases [82]
STRING (Search Tool for the Retrieval of Interacting Genes/Proteins) Swiss Institute of Bioinformatics, Switzerland STRING is a database of known and predicted protein–protein interactions. The interactions include direct (physical) and indirect (functional) associations; they stem from computational prediction, from knowledge transfer between organisms, and from interactions aggregated from other (primary) databases [83]
TTD (Therapeutic Target Database) Department of Computational Science National University of Singapore, Singapore Therapeutic target database (TTD) is a database to provide information about the known and explored therapeutic protein and nucleic acid targets, the targeted disease, pathway information and the corresponding drugs directed at each of these targets. Also included in this database are links to relevant databases containing information about target function, sequence, 3D structure, ligand binding properties, enzyme nomenclature and drug structure, therapeutic class, clinical development status. All information provided are fully referenced [84]
Uniprot (Univeral Protein) UniProt Consortium The Universal Protein Resource (UniProt) is a comprehensive resource for protein sequence and annotation data. The UniProt databases are the UniProt Knowledgebase (UniProtKB), the UniProt Reference Clusters (UniRef), and the UniProt Archive (UniParc) [67]