Background
| BOND | |
|---|---|
| Developer(s) | Christopher Hogue et al., Samuel Lunenfeld Research Institute, Mount Sinai. Commercial rights: Unleashed Informatics |
| Stable release | BIND 4.0, SMIDsuite
|
| Type | Bioinformatics tool |
| License | Open Access |
| Website | [1] |
The Blueprint Initiative started as a research program in the lab of Dr. Christopher Hogue the Samuel Lunenfeld Research Institute at Mount Sinai in Toronto. On December 14, 2005 Unleashed Informatics Limited acquired the commercial rights to The Blueprint Initiative intellectual property. This included rights to the protein interaction database BIND, the small molecule interaction database SMID, as well as the data warehouse SeqHound. Unleashed Informatics is a data management service provider and is overseeing the management and curation of The Blueprint Initiative under the guidance of Dr. Hogue[1].
Biomolecular Object Network Databank (BOND)
The Biomolecular Object Network Databank, which integrates the original blueprint initiative databases as well as other databases, such as Genbank, combined with many tools required to analyze these data. Annotations links for sequences, including taxon identifiers, redundant sequences, Genome Ontology descriptions, Online Mendelian Inheritance in Man identifiers, conserved domains, data base cross-references, LocusLink Identifiers and complete genomes are also available. Bond facilitates cross-database queries and is an open access resource which integrates interaction and sequence data[2].
Small Molecule Interaction Database (SMID)
The Small Molecule Interaction Database is a database containing protein ___domain-small molecule interactions. It uses a ___domain-based approach to identify ___domain families, found in the Conserved Domain Database (CCD), which interact with a query small molecule. The CCD from NCBI amalgamates data from several different sources; Protein FAMilies (PFAM), Simple Modular Architecture Research Tool (SMART), Cluster of Orthologous Genes (COGs), and NCBI’s own curated sequences. The data in SMID is derived from the Protein Data Bank (PDB), a database of known protein crystal structures. SMID can be queried by entering a protein GI, ___domain identifier, PDB ID or SMID ID. The results of a search provide small molecule, protein, and ___domain information for each interaction identified in the database. Interactions with non biological contacts are normally screened out by default.
SMID-BLAST is a tool developed to annotate known small-molecule binding sites as well as to predict binding sites in proteins whose crystal structures have not yet been determined. The prediction is based on extrapolation of known interactions, found in the PDB, to interactions between an uncrystallized protein with a small molecule of interest. SMID-BLAST was validated against a test set of known small molecule interactions from the PDB. It was shown to be an accurate predictor of protein-small molecule; 60% of predicted interactions identically matched the PDB annotated binding site, and of these 73% had greater than 80% of the binding residues of the protein correctly identified. Hogue, C et al. estimated that 45% of predictions that were not observed in the PDB data do in fact represent true positives[3].
Biomolecular Interaction Network Database (BIND)
User Statistics
The number of Unleashed Registrants has increased 10 fold since the integration of BIND. As of December 2006 registration fell just short of 10,000. Subscribers to the commercial versions of BOND fall into six general categories; agriculture and food, biotech, pharmaceuticals, informatics, materials and other. The biotechnology sector is the largest of these groups, holding 28% of subscriptions. Pharmaceuticals and informatics follow with 22% and 18% respectively. The United States holds the bulk of these subscriptions, 69%. Other countries with access to the commercial versions of BOND include Canada, the United Kingdom, Japan, China, Korea, Germany, France, India and Australia. All of these countries fall below 6% in user share[2].
1. www.blueprint.org
2. bond.unleashedinformatics.com
3. Snyder, K et al. Domain-based small molecule binding site annotation. BMC Bioinformatics. 7: 152 (2006).