Biomolecular Object Network Databank: Difference between revisions

Revision as of 14:38, 16 May 2009

Revision as of 17:24, 17 May 2009

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The '''Biomolecular Object Network Databank''' ('''BOND''') is a bioinformatics databank containing information on [[small molecule]] and protein sequences, structures and interactions. The databank integrates a number of existing databses to provide a comprehensive overview of the information currently available for a given molecule.

==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]}}

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==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 (publishing)|open access]] resource which integrates interaction and sequence data. <ref name= "BOND">[http://bond.unleashedinformatics.com BOND at Unleashed Informatics]</ref>

==Small Molecule Interaction Database (SMID)==

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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. <ref>Snyder, K, ''et al.''. Domain-based small molecule binding site annotation. BMC Bioinformatics 7: 152 (2006)</ref>

==Biomolecular Interaction Network Database (BIND)==

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BIND has grown significantly since its conception; in fact, the database saw a 10 fold increase in entries between 2003 and 2004. By September 2004, there were over 100,000 interaction records by 2004 (including 58,266 protein-protein, 4,225 genetic, 874 protein-small molecule, 25,857 protein-DNA, and 19,348 biopolymer interactions). The database also contains sequence information for 31,972 proteins, 4560 DNA samples and 759 RNA samples. These entries have been collected from 11,649 publications; therefore, the database represents an important amalgamation of data. The organisms with entries in the database include: ''[[Saccharomyces cerevisiae]]'', ''[[Drosophila melanogaster]]'', ''[[Homo sapiens]]'', ''[[Mus musculus]]'', ''[[Caenorhabditis elegans]]'', ''[[Helicobacter pylori]]'', ''[[Bos taurus]]'', [[HIV-1]], ''[[Gallus gallus]]'', ''[[Arabidopsis thaliana]]'', as well as others. In total, 901 [[taxa]] were included by September 2004 and BIND has been split up into BIND-Metazoa, BIND-Fungi, and BIND-Taxroot.<ref name= "2005 update"/>

Not only is the information contained within the database continually updated, the software itself has gone through several revisions. Version 1.0 of BIND was released in 1999 and based on user feedback it was modified to include additional detail on experimental conditions required for binding and a hierarchical description of cellular ___location of the interaction. Version 2.0 was released in 2001 and included the capability to link to information available in other databases.<ref name= "BIND, 2001"/> Version 3.0 (2002) expanded the database from physical/biochemical interactions to also include genetic interactions.<ref name= "BIND, 2003">Bader, GD, ''et al.''. BIND: the Biomolecular Interaction Network Database. ''Nucleic Acids Research'' 31: 248-250 (2003).</ref> Version 3.5 (2004) included a refined user-interface that aimed to simplify information retrieval.<ref name= "2005 update"/> In 2006, BIND was incorporated into the Biomolecular Object Network Database (BOND) where it continues to be updated and improved.

===Special features===

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===Accessing the database===

[[Image:Copy of BIND Screen.JPG|thumb|Figure 1: Screen shot of sequence results obtained using BOND ]]

The database user interface is web-based and can be queried using text or accession numbers/identifiers. Since its integration with the other components of BOND, sequences have been added to interactions, molecular complexes and pathways in the results. Records include information on: BIND ID, description of the interaction/complex/pathway, publications, update records, organism, OntoGlyphs, ProteoGlyphs, and links to other databases where additional information can be found. BIND records include various viewing formats (e.g. [[HTML]], [[ASN.1]], [[XML]], [[FASTA]]), various formats for exporting results (e.g. ASN.1, [[XML]], [[GI list]], [[PDF]]), and visualizations (e.g. [[Cytoscape]]). The exact viewing and exporting options vary depending on what type of data has been retrieved.

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<references />

[[Category: Bioinformatics databases]]

[[Category: Bioinformatics databases]]