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Abstract

We are developing solutions to two major problems in protein crystallography:

1. The elucidation of protein structures at atomic resolution is computationally demanding and requires user-friendly interfaces to high-performance computing resources. Fortunately, critical calculations are embarrassingly parallel and thus ideally suited to distributed computing. We discuss how we are using grid computing to determine the three dimensional structures of proteins using the technique of Molecular Replacement in a massively parallel fashion, in a timeframe of minutes to hours - orders of magnitude faster than is currently possible.
   
2. There is a pressing need for the archiving and curation of raw X-ray diffraction data. This information is critical for validation, methods development and improvement of archived structures. However, the relatively large size of these datasets has presented challenges for storage in a single worldwide repository, such as the the Protein Data Bank. This problem can be avoided by using a federated approach, where each institution utilizes its institutional repository for storage, with a discovery service overlaid. Institutional repositories are relatively stable and adequately funded, ensuring persistence. Here we describe a simple repository solution, utilizing Fedora open source database software, and data annotation and deposition tools that can be deployed at any site cheaply and easily. Datasets and associated metadata from federated repositories are given a unique and persistent handle, providing a simple mechanism for search and retrieval via web interfaces. In addition to ensuring that valuable data is not lost, the provision of raw data has several uses for the crystallographic community. Most importantly, structure determination can only be truly repeated or verified once the raw data is available. Moreover, the availability of raw data is extremely useful for the development of improved methods of image analysis and data processing. We call this initiative ‘The Australian Repositories for Diffraction Images (TARDIS)’ and have created a website (http://www.tardis.edu.au) where the deposition tools can be downloaded freely.

About the speaker

Ashley Buckle completed his PhD in 1994 in the lab of Prof Sir Alan Fersht at Cambridge University, where he focused his research on the structure determination of protein- DNA and protein-protein complexes. As a postdoctoral then staff scientist at the MRC Centre Cambridge, he made contributions to the understanding of protein stability, molecular recognition and the action of molecular chaperones. He relocated to Monash in 2003 and is currently an NHMRC Senior Research Fellow. His current research is split between structural studies of a variety of interesting biological systems (using protein crystallography), crystallographic methods development, and bioinformatics.