The Biomolecular Object Network Databank is a bioinformatics databank containing information on small molecule structures and interactions. The databank integrates a number of existing databases to provide a comprehensive overview of the information currently available for a given molecule.
Background
The Blueprint Initiative started as a research program in the lab of Dr. Christopher Hogue at the Samuel Lunenfeld Research Institute at Mount Sinai Hospital 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.
Construction
BOND integrates the original Blueprint Initiative databases as well as other databases, such as Genbank, combined with many tools required to analyze these data. Annotation links for sequences, including taxon identifiers, redundant sequences, Gene 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.
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 (CDD), which interact with a query small molecule. The CDD 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 interactions; 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.
Biomolecular Interaction Network Database (BIND)
Introduction
The idea of a database to document all known molecular interactions was originally put forth by Tony Pawson in the 1990s and was later developed by scientists at the University of Toronto in collaboration with the University of British Columbia. The development of the Biomolecular Interaction Network Database (BIND) has been supported by grants from the Canadian Institutes of Health Research (CIHR), Genome Canada, the Canadian Foundation for Innovation and the Ontario Research and Development Fund. BIND was originally designed to be a constantly growing depository for information regarding biomolecular interactions, molecular complexes and pathways. As proteomics is a rapidly advancing field, there is a need to have information from scientific journals readily available to researchers. BIND facilitates the understanding of molecular interactions and pathways involved in cellular processes and will eventually give scientists a better understanding of developmental processes and disease pathogenesis