BIND: the Biomolecular Interaction Network Database

Abstract

The Biomolecular Interaction Network Database (BIND: http://bind.ca) archives biomolecular interaction, complex and pathway information. A web-based system is available to query, view and submit records. BIND continues to grow with the addition of individual submissions as well as interaction data from the PDB and a number of large-scale interaction and complex mapping experiments using yeast two hybrid, mass spectrometry, genetic interactions and phage display. We have developed a new graphical analysis tool that provides users with a view of the domain composition of proteins in interaction and complex records to help relate functional domains to protein interactions. An interaction network clustering tool has also been developed to help focus on regions of interest. Continued input from users has helped further mature the BIND data specification, which now includes the ability to store detailed information about genetic interactions. The BIND data specification is available as ASN.1 and XML DTD.

Figure 1

Functional Alignment Search Tool (FAST). Domain composition for a set of proteins that interact with mouse Fyn is shown as uniquely coloured horizontal bars above a line representing the sequence. Expanded view of Vav, linked to via right-pointing red arrows, where domains are shown correctly situated on the amino acid sequence of each protein. For brevity, this figure does not show all Fyn-interacting proteins in BIND or, in the expanded view, all of the domains in Vav.