From: Systems biology approaches for advancing the discovery of effective drug combinations
Application | Resource | Description | URL |
---|---|---|---|
Drug data | PubChem | Database of biological activities of millions of small molecules. | |
 | DrugBank | Database of target, chemical, pharmacological, and interaction data for 7739 drugs. | |
 | STITCH | Chemical-protein interaction database containing 300,000 small molecules and 2.6 million proteins from 1133 organisms. | |
 | SIDER | Database of adverse drug reactions from marketed medicines. | |
 | Comparative Toxicogenomics Database (CTD) | Manually curated database of over a million interactions between chemicals and genes and over 1.6 million associations between chemicals and diseases and over 15 million associations between genes and diseases. | |
 | PharmGKB | Database of drug information including dosing guidelines, drug labels, signaling pathway diagrams, drug-gene associations, and drug-phenotype relationships. | |
 | Drug Gene Interaction Database (DGIdb) | Database and web tool for mining over 14,000 drug-gene relationships. | |
Drug combinations | Drug Combination Database (DCDB) | Data from 1363 drug combinations. | |
Protein-protein interactions | BioGrid | Database of over 720,000 protein and genetic interactions from model organisms and humans from over 41,000 publications. | |
 | STRING | Database of known and predicted protein interactions, including both direct and functional associations. It currently covers 5,214,234 proteins from 1133 organisms. | |
Gene expression data | Connectivity Map (CMap) | Gene expression profiles from 1309 FDA approved small molecules tested in 5 human cell lines. | |
 | Gene Expression Omnibus (GEO) | Public repository of gene expression data. | |
Kinase inhibitors | K-Map | Web tool that identifies kinase inhibitors for a set of query kinases. | |
Pathways | Reactome | Pathway database with visual representation for 21 organisms, which includes over 1500 human pathways. | |
 | KEGG Pathways | Large collection of manually drawn pathway maps of molecular interaction networks for various biological processes. | |
Network visualization | Cytoscape | Open source software platform for network analysis and visualization. | |
Computational modeling | Netflux | Modeling and simulation tool for construction of normalized-Hill models of signaling networks from user defined species interactions. | |
 | CellNOpt | Free software for creating logic-based models of signaling networks. | |
 | BioModels Database | Repository of computational models of biological processes. Includes both peer-reviewed models and models produced automatically using pathway resources like KEGG. | |
Experimental resources | Cancer Cell Line Encyclopedia | Detailed genetic characterization of ~1000 cancer cell lines. | |
 | Genomics of Drug Sensitivity in Cancer (GDSC) | Drug sensitivity data from hundreds of genetically characterized cancer cell lines perturbed with a wide variety of anti-cancer agents Part of an ongoing project to discover therapeutic biomarkers. | |
 | NCI-60 DTP | Drug screen data from a diverse panel of 60 human cancer cell lines with extensive molecular profiling. | |
 | Cancer Therapeutics Response Portal | Drug sensitivity data of 242 genetically characterized cancer cell lines treated with 354 different small molecule probes and drugs. Each compound selectively targets a distinct part of cell wiring and collectively affect a vast array of cell processes. |