Extending a molecular docking tool to run simulations on clouds Damjan Temelkovski Dr. Tamas Kiss...
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Transcript of Extending a molecular docking tool to run simulations on clouds Damjan Temelkovski Dr. Tamas Kiss...
Extending a molecular docking tool to run simulations on clouds
Damjan TemelkovskiDr. Tamas Kiss
Dr. Gabor Terstyanszky
University of Westminster
Molecular Dockinga.k.a. in-silico docking
Simulating the interaction between two molecules: • a ligand (small molecule)• a receptor (protein)
Predicting the binding affinity and the conformation
Popular tools: • Autodock*• Autodock Vina*• GOLD• FlexX• SwissDock• HADDOCK
*most popular, tool of choice at University of Westminster
Virtual Screening Reverse Docking
L1
L2
L3
L4
L5
R1 L1
R2
R4
R3
R1
History of Virtual Screening at UoW
Manually running the softwareManually writing scripts
Too slow Too complicated
gUSE portal on desktop grid (private @UoW, public @SZTAKI)
Selected scenarios only, too restrictive
Raccoon (generate scripts automatically):Run locallyRun on a PBS cluster
Too slowToo complicated
One solution:
Extend Raccoon to run jobs through the RemoteAPI of gUSE
enabling execution on clouds, grids, supercomputers with minimal changes to the GUI
From the point of view of life scientists
• Approach 1: standalone Raccoon job
• Approach 2: dissect Raccoon to run in parallel
Raccoon prepares all files for the simulation, but the execution would be sequential
1) Run AutoGrid at each job (per ligand-receptor pair)
2)* Run AutoGrid now (per receptor)
3) Don’t run AutoGrid
• Approach 2b: run prepare_g(d)pf locally – work in progress
Result
• Small extension of GUI
• workflow.xml updated in code to reflect the number of paramInputs
• Zip all properly named input files and submit
• Download results when finished
The Big Picture
• PhD research: Analysis of Big Data from Molecular Simulations
Data Collection
• Raccoon via gUSE RemoteAPI• Desktop grid portals• Manually running Autodock• Manually running other tools• Via environments for other tools
Provenance Management
Result Repository
Analyse
Validate
Questions
?