Table 5.
Chemical compound similarity networks
| Basis of chemical compound similarity | References |
|---|---|
| chemical compound similarity networks | |
| chemical similarity based on e.g. the Tanimoto-coefficient QSAR-related similarity networks (a freely available program to mine structure-activity and structure-selectivity relationship information in compound data sets, SARANEA: http://www.limes.uni-bonn.de/forschung/abteilungen/Bajorath/labwebsite/downloads/saranea/view) | Tanaka et al., 2009; Bickerton et al., 2012 Estrada et al., 2006; García et al., 2009; Gonzalez-Diaz & Prado-Prado, 2008; Hert et al., 2008; Prado-Prado et al., 2008; Wawer et al., 2008; Bajorath et al., 2009; Prado-Prado et al., 2009; Gonzalez-Diaz et al., 2010a; Lounkine et al., 2010; Peltason et al., 2010; Prado-Prado et al., 2010; Wawer et al., 2010; Iyer et al., 2011a; Iyer et al., 2011b; Iyer et al., 2011c; Krein & Sukumar, 2011; Wawer & Bajorath, 2011a; Wawer & Bajorath, 2011b |
| BioAssay network: bioassay data of chemical compounds from PubChem | Zhang et al., 2011b |
| similarity of protein binding sites | Paolini et al., 2006; Keiser et al., 2007; Hert el al., 2008; Park & Kim, 2008; Adams et al., 2009; Keiser et al., 2009; Hu et al., 2011 |
| network of drug-receptor pairs with multitarget QSAR | Vina al., 2009 |
| CARLSBAD: a Cytoscape plug-in for connecting common chemical patterns to biological targets via small molecules http://carlsbad.health.unm.edu | |
| drug-target network combined with the chemical structure network of the drug and the protein structure network of its target giving quality-scores of drug-target networks | Riera-Fernández et al., 2012 |
| similarity of mRNA expression profiles extended with disease mRNA expression profiles: Connectivity Map http://www.broadinstitute.org/cmap | Lamb et al., 2006; Iorio et al., 2009; Huang et al., 2010a |
| side-effect similarity of drugs | Campillos et al., 2008 |
| protein-protein interaction network topology of the target neighborhood (a database of more than 700,000 chemicals, 30,000 proteins and their over 2 million interactions integrated to a human protein-protein interaction network having over 400,000 interactions, ChemProt: http://www.cbs.dtu.dk/services/ChemProt) | Hansen et al., 2009; Li et al., 2009a; Taboreau et al., 2011; Edberg et al., 2012 |
| integrated bio-entity relationship datasets and networks | |
| structural similarity, QSAR, gene-disease interactions, biological processes, drug absorption, distribution, metabolism and excretion (ADME) data and toxicity mechanisms | Brennan et al., 2009 |
| integrated semantic network of chemogenomic repoitories, Chem2Bio2RDF http://cheminfov.informatics.indiana.edu:8080 | Chen et al., 2010 |
| drug therapeutic and chemical similarity with protein-protein interaction network data: drugCIPHER | Zhao & Li, 2010 |
| protein-protein interactions, protein/gene regulations, protein-small molecule interactions, protein-Gene Ontology relationships, protein-pathway relationships and pathway-disease relationships: bio-entity network (IBN) | Bell et al., 2011 |
| phenotype/single-nucleotide polymorphism (SNP) associations, protein-protein interactions, disease-tissue, tissue-gene and drug-gene relationships: integrated Complex Traits Networks, iCTNet Cytoscape plug-in, http://flux.cs.queensu.ca/ictnet | Wang et al., 2011b |
| protein-protein interactions, protein-small molecule interactions, associations of interactions with pathways, species, diseases and Gene Ontology terms with the user-selected integration of manually curated and/or automatically extracted data: integrated molecular interaction database, IMID, http://integrativebiology.org | Balaji et al., 2012 |