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Nucleic Acids Research, 2001, Vol. 29, No. 1 242-245
© 2001 Oxford University Press

BIND—The Biomolecular Interaction Network Database

Gary D. Bader1,2, Ian Donaldson2, Cheryl Wolting2, B. F. Francis Ouellette3, Tony Pawson2,4 and Christopher W. V. Hogue1,2,*

1Department of Biochemistry, University of Toronto, Canada, 2Samuel Lunenfeld Research Institute, Toronto, M5G 1X5, Canada, 3Centre for Molecular Medicine and Therapeutics, Children’s and Women’s Health Centre of British Columbia, University of British Columbia, Vancouver, V5Z 4H4, Canada and 4Department of Molecular and Medical Genetics, University of Toronto, Canada

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.

* To whom correspondence should be addressed at: Room 1060, Samuel Lunenfeld Research Institute, 600 University Avenue, Toronto M5G 1X5, Canada. Tel: +1 416 586 4800; Fax: +1 416 586 8869; Email: hogue{at}mshri.on.ca


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