PRAGMA: Grid Interoperation for Biomedically-Relevant Protein Structures

As e-Science continues to be embraced by the wider research community, the demand for resources also increases, particularly the need to interoperate Grids. PRAGMA members developed a case study to test Grid interoperability and interoperation.

To ensure the validity and relevance of its study, a real science application was run – a Nimrod/G experiment in structural biology. Specifically, multiple conformations of multiple proteins from the Protein Data Bank (PDB) were used in a protein crystal structure determination, using the Molecular Replacement (MR) technique. This involved testing the entire PDB using the MR application PHASER www-structmed.cimr.cam.ac.uk/phaser, a maximum likelihood approach.

This experiment generated more than 70,000 executions across five Grids, requiring over half a million CPU hours. The team performed MR calculations using the entire PDB (~80,000 structures) in a reasonable timeframe. This feat was inconceivable three years ago (and many in the application community consider it still is). PRAGMA’s approach has led to the structural solution of several key medically important proteins in laboratories, many of which involve collaborations with researchers from Monash University and several international laboratories, which would otherwise have remained unsolved. Much of this data is currently being published in top international journals.

URL:

www.pragma-grid.net/wp-content/PRAGMA2008.pdf

Collaborators:

USA:
University of California, San Diego; Renaissance Computing Institute (RENCI); Pacific Rim Applications and Grid Middleware Assembly (PRAGMA) Grid; FermiGrid; Open Science Grid

Australia:
Monash University; Australian EnterpriseGrid; APAC Grid

Switzerland:
University of Zurich