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3D Crunch Project Could Predict Thousands of New Protein Structures

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CORTAILLOD, Switzerland--Silicon Graphics, in collaboration with bioinformatics and protein modeling experts at Glaxo Well come, the Imperial Cancer Re search Fund, the Swiss Institute of Bioinformatics, and Lyon Bioinformatics Center at University Claude Bernard, May 18 launched a week-long project aimed at analyzing more than 200,000 public protein sequences and predicting 50,000 new 3D protein structures. The resulting database will be made available to the public through participants' web sites.

Dubbed "3D Crunch," the project is relying on a Silicon Graphics Cray Origin2000 server located at the Silicon Graphics European Advanced Technology Center here, and on software developed by bioinformaticists at the collaborating organizations. The 64-processor server will power SWISS-MODEL, 3D protein modeling software developed by Glaxo Wellcome's worldwide director of scientific computing, Manuel Peitsch, and his research team. The program will analyze the 200,000 public protein sequences in the SWISS-PROT and TrEMBL databases and predict their 3D structures by comparing them to related proteins with known structures stored in the Protein Databank, with 11 mirror sites around the world.

For sequences that cannot be predicted by SWISS-MODEL, software and databases developed at the Imperial Cancer Research Fund and the Lyon Bioinformatics Center will be used. FOLDFIT, developed by the Imperial Fund with Glaxo Wellcome, will be used to suggest a function for the bacterial protein sequences in the databases that cannot be modeled with comparative methods.

Peitsch said the server allows a year of computing time to be compressed down to a week. He explained, "Most of the 4,500 protein structures available to the world have been generated by the difficult and time-consuming work required in traditional laboratory methods. 3D Crunch will provide a significantly larger resource of computationally-generated structural information to researchers."

Paul Nurse, director of the Imperial Fund in London said the project would give insights into the molecular basis of human diseases.

In 1996, Silicon Graphics with the European Molecular Biology Labor atory and the European Bioinfor matics Institute conducted a Gene Crunch analysis project on the web. SpaceCrunch was another Silicon Graphics project--this time done with Tripos--that let scientists search a virtual combinatorial chemistry database online.

The 3D Crunch websites include: Silicon Graphics at http://www.sgi.com/chembio; Glaxo Well come at http://www.glaxowellcome.co.uk; Imperial Cancer Research Fund at http://www.icnet.uk/bmm; and Swiss Institute of Bioinformatics at http://www.expaswy.ch.

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