The Biomolecular Interaction Network Database (BIND; http://binddb.org) is
a database designed to store full descriptions of interactions, molecular c
omplexes and pathways. Development of the BIND 2.0 data model has led to th
e incorporation of virtually all components of molecular mechanisms includi
ng interactions between any two molecules composed of proteins, nucleic aci
ds and small molecules. Chemical reactions, photochemical activation and co
nformational 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 a
nd to generate information for kinetic simulations. BIND anticipates the co
ming large influx of interaction information from high-throughput proteomic
s efforts including detailed information about post-translational modificat
ions from mass spectrometry. Version 2.0 of the BIND data model is discusse
d as well as implementation, content and the open nature of the BIND projec
t. The BIND data specification is available as ASN.1 and XML DTD.