Biomolecular Object Network Databank: Difference between revisions

Revision as of 17:37, 5 September 2011

Revision as of 18:48, 20 January 2012

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==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 [[National Center for Biotechnology Information|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.

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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 [[Anthony Pawson|Tony Pawson]] in the 1990’s1990s 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 (publishing)|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.