Research Project

Website: http://www.bind.ca

Summary

Human Genome Project researchers around the world produce a huge amount of raw information about genes and proteins. This material needs processing if it is to be useful for further studies and for practical applications. People must organize it into databases, analyse it in many ways, and above all make it available to researchers everywhere.

This project team set up specialized databases for genomic researchers everywhere.  The first database - BIND - contains information for over 200,000 protein and DNA interactions, which are the biological processes that drive living cells and are central to biological and medical research. The second -  SMID - details over 13 million chemical binding sites on protein molecules; these can help researchers  identify medical and industrial applications for chemicals that  alter proteins active  in biological processes. A third - SeqHound - contains raw information from the Human Genome Project on which the team built BIND and SMID. The team screened the material in these databases meticulously to be sure of its very high quality.  It also created a large set of software tools that enable many kinds of analysis of the information in these databases.

Thousands of biomedical researchers all over the world use these databases to discover new connections among genes and proteins that they might otherwise have missed. This reduces the cost and time of research and leads to better understanding of how cells work. Using BIND and SMID gives scientists the possibility of designing new drugs to treat many diseases.

Fast Facts

• Highlighted outcome:  Databases that contain crucial data on molecular interaction that biomedical researchers everywhere can use.
• Number of research personnel:  More than 100.
• Number of peer-reviewed publications:  20 plus 48 invited presentations and hundreds of publications that used the databases.
• Number of patents in process or obtained: 1.
• Resources generated: BIND, SeqHound, and SMID databases for public use plus a large set of analytical software.
• Number of public outreach events:  30.

Notable Publications
Alfarano C, Andrade CE, Anthony K, Bahroos N, Bajec M, Bantoft K, Betel D, Bobechko B, Boutilier K, Burgess E, Buzadzija K, Cavero R, D'Abreo C, Donaldson I, Dorairajoo D, Dumontier MJ, Dumontier MR, Earles V, Farrall R, Feldman H, Garderman E, Gong Y, Gonzaga R, Grytsan V, Gryz E, Gu V, Haldorsen E, Halupa A, Haw R, Hrvojic A, Hurrell L, Isserlin R, Jack F, Juma F, Khan A, Kon T, Konopinsky S, Le V, Lee E, Ling S, Magidin M, Moniakis J, Montojo J, Moore S, Muskat B, Ng I, Paraiso JP, Parker B, Pintilie G, Pirone R, Salama JJ, Sgro S, Shan T, Shu Y, Siew J, Skinner D, Snyder K, Stasiuk R, Strumpf D, Tuekam B, Tao S, Wang Z, White M, Willis R, Wolting C, Wong S, Wrong A, Xin C, Yao R, Yates B, Zhang S, Zheng K, Pawson T, Ouellette BF, and Hogue CW. 2005.  The Biomolecular Interaction Network Database and related tools 2005 update. Nucleic Acids Res. 33 (Database issue):D418-24.

Donaldson I, Martin J, de Bruijn B, Wolting C, Lay V, Tuekam B, Zhang S, Baskin B, Bader GD, Michalickova K, Pawson T, and Hogue CW. 2003.  PreBIND and Textomy - mining the biomedical literature for protein--protein interactions using a support vector machine. BMC Bioinformatics 4:11.

Snyder KA, Feldman HJ, Dumontier M, Salama JJ, and Hogue CW. 2006.  Domain-based small molecule binding site annotation. BMC Bioinformatics 17(&):152.

Feldman HJ, Snyder KA, Ticoll A, Pintilie G, and Hogue CW.2006.  A complete small molecule dataset from the protein data bank. FEBS Lett. 580(6):1649-53.

Snyder KA, Feldman HJ, Dumontier M, Salama JJ, and Hogue CW. 2006.  Domain-based small molecule binding site annotation. BMC Bioinformatics 7:152.