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High-Throughput Crystallography at Monash
Noel Faux
Dept of Biochemistry
and Molecular Biology
Monash University
Structural Biology Pipe Line
QuickTime™ and aTIFF (Uncompressed) decompressor
are needed to see this picture.
CloningExpression
PurificationCrystallisation
X-ray diffraction Determine the structure
High throughput robots and technologies:Tecan Freedom EvolutionÄKTAxpress™Trialing crystal storage and imaging facilities
Australian synchrotrononline in 2007
Data processingand structural determination: major bottle neck
Target tracking / LIMSData
ManagementPhasing (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
Instrume
nt R
epK
epler
Crystal Temp
Lab Temp
X-ray image
Mounted crystal Streaming Video (SV)
Lab SV
Lab Still Pics
Sensor Data
Storage ResourceBroker
Monash University ITs Sun GRID: 54 dual 2.3 GHz CPUs208.7 GB (3.8 GB per node)>10 TB storage capacityRunning Gridsphere
Lab PC
CollectionPC
Central web portal
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, 760-763.
1
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, 458-464. 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
ClassFold
SuperfamilyFamilies
Domains
7971
15893004
75930
• 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 OpteronCPUs208.7 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
QuickTime™ and aTIFF (Uncompressed) decompressor
are needed to see this picture.
CloningExpression
PurificationCrystallisation
X-ray diffraction Determine the structure
Data collection, management, storage, and remote accessDART
Xia2 Data processing, exhaustive experimental (e.g., SAD, SIRAS, MIRAS) and MR phasing for final refinementGrid ComputingNIMRODPHASERAutoSHARPCCP4DART
High through put robotics and
technologies
AcknowledgmentsMonash UniversityAnthony BeitzNicholas McPheeJames WhisstockAshley Buckle
James Cook UniversityFrank EilertTristan King
DART Team