BIND--The Biomolecular Interaction Network Database

Abstract

The Biomolecular Interaction Network Database (BIND; http://binddb. org) is a database designed to store full descriptions of interactions, molecular complexes and pathways. Development of the BIND 2.0 data model has led to the incorporation of virtually all components of molecular mechanisms including interactions between any two molecules composed of proteins, nucleic acids and small molecules. Chemical reactions, photochemical activation and conformational changes can also be described. Everything from small molecule biochemistry to signal transduction is abstracted in such a way that graph theory methods may be applied for data mining. The database can be used to study networks of interactions, to map pathways across taxonomic branches and to generate information for kinetic simulations. BIND anticipates the coming large influx of interaction information from high-throughput proteomics efforts including detailed information about post-translational modifications from mass spectrometry. Version 2.0 of the BIND data model is discussed as well as implementation, content and the open nature of the BIND project. The BIND data specification is available as ASN.1 and XML DTD.

Figure 1

BIND Interaction Viewer Java applet showing how molecules can be connected in the database from molecular complex to small molecule. Yellow, protein; purple, small molecule; white, molecular complex; red, a square is fixed in place and will not be moved by the graph layout algorithm. This session was seeded by the interaction between human LAT and Grb2 proteins involved in cell signaling in the T-cell.