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The '''Biomolecular Object Network Databank''' ('''BOND''') is a
==Background==
{{Infobox Software|name=BOND|developer=Christopher Hogue et al., Samuel Lunenfeld Research Institute, Mount Sinai. Commercial rights: Unleashed Informatics|latest_release_version=BIND 4.0, SMIDsuite|genre=Bioinformatics tool|license=Open Access|website=[http://bond.unleashedinformatics.com/index.jsp?pg=0]}}
The
==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
==Small Molecule Interaction Database (SMID)==
The Small Molecule Interaction Database is a database containing protein ___domain-small molecule interactions. It uses a
SMID can be queried by entering a
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[3].
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==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 1990’s 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
The major goals of the BIND project are: to create a public proteomics resource that is available to all; to create a platform to enable [[datamining]] from other sources (PreBIND); to create a platform capable of presenting visualizations of complex molecular interactions. From the beginning, BIND has been [[open access]] and software can be freely distributed and modified. Currently, BIND includes a data specification, a database and associated data mining and visualization tools. Eventually, it is hoped that BIND will be a collection of all the interactions occurring in each of the major model organisms.
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==User statistics==
The number of
==References==
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