High-Throughput Crystallography at Monash Noel Faux Dept of Biochemistry and Molecular Biology Monash University

Structural Biology Pipe Line Cloning Expression Purification Crystallisation X-ray diffractionDetermine the structure High throughput robots and technologies: Tecan Freedom Evolution ÄKTAxpress™ Trialing crystal storage and imaging facilities Australian synchrotron online in 2007 Data processing and structural determination: major bottle neck Target tracking / LIMS Data Management Phasing ( CCP4/CNS GRID computing )

The problems Target-tracking/Data management The process of protein structure determination creates a large volume of data. Storage, security, traceability, management and backup of files is ad-hoc. Remote access of the files is limited and requires different media formats. Structure determination CPU intensive

Part of a National Project for the development of eResearch platforms for the management and analysis of data for research groups in Australia. Aim: establish common standardised software / middleware applications that are adaptable to many research capabilities

Solution Central repository of files Attach metadata to the files World wide secure access to the files Automated collection and annotation of the files from in-house and synchrotron detectors

The infrastructure Instrument Rep Kepler Crystal Temp Lab Temp X-ray image Mounted crystal Streaming Video (SV) Lab SV Lab Still Pics Sensor Data Storage Resource Broker Monash University ITs Sun GRID: 54 dual 2.3 GHz CPUs GB (3.8 GB per node) >10 TB storage capacity Running Gridsphere Lab PC Collection PC

Central web portal

Automated X-ray data reduction Automated processing of the diffraction data Investigating the incorporation of Xia2 : Automated Data Reduction: New automated data reduction system designed to work from raw diffraction data and a little metadata, and produce usefully reduced data in a form suitable for immediately starting phasing and structure determination (CCP4) 1. (Graeme Winter) The CCP4 suite: programs for protein crystallography. (1994). Acta Crystallogr. D50,

Divide and Conquer A large number of CPUs available across different computer clusters at different locations: Monash ITs Sun grid VPAC: (Brecca – 97 dual Xeon 2.8 GHz CPUs, 160 GB (2 GB per node) total memory; Edda – 185 Power5 CPUs, 552 GB (8-16 GB per node) total memory) APAC: 1680 processors, 3.56 terabytes of memory, 100 terabytes of disk Personal computers

DART and CCP4 Aims: Use the CCP4 interface locally but run the jobs remotely across a distributed system Nimrod to distribute the CCP4 jobs across the different Grid systems Investigating the possibility of incorporating the CCP4 interface into the DART web portal

No phasing data No sequence identity (<20%) No search model Is there a possible fold homolog Exhaustive Phaser scan of the PDB Exhaustive searches with different parameters and search models Exhaustive Molecular Replacement 2. Acta Cryst. (2005). D61, Likelihood-enhanced fast translation functions A. J. McCoy, R. W. Grosse-Kunstleve, L. C. Storoni and R. J. Read. 2

Exhaustive Molecular Replacement Proteins building blocks are domains Use subset of SCOP as search models in a PHASER calculation. The use of Grid computing will make this possible ~1000 CPUs = days for typical run SCOP Class Fold Superfamily Families Domains Search at the family level Take the highest resolution structure Mutate to poly-alanine, and delete loops and turns Phaser Families with z-score  6 search with each of their domain members

Exhaustive Molecular Replacement Database containing: ToDo list Parameters Results ITs Sun GRID Each node runs a perl script: Requests a job Launch phaser Returns the results Repeats until the list is exhausted 56 dual dual AMD OpteronCPUs GB (3.8 GB per node) >10 TB storage capacity, 160 GB (2 GB per node) total memory Will be extended to use Nimrod to gain access to APAC and the Pacific Rim Grid (Pragma)

Final Pipeline Cloning Expression Purification Crystallisation X-ray diffractionDetermine the structure Data collection, management, storage, and remote access DART Xia2 Data processing, exhaustive experimental (e.g., SAD, SIRAS, MIRAS) and MR phasing for final refinement Grid Computing NIMROD PHASER AutoSHARP CCP4 DART High through put robotics and technologies

Acknowledgments Monash University Anthony Beitz Nicholas McPhee James Whisstock Ashley Buckle James Cook University Frank Eilert Tristan King DART Team