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Extending a molecular docking tool to run simulations on clouds Damjan Temelkovski Dr. Tamas Kiss...
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![Page 1: Extending a molecular docking tool to run simulations on clouds Damjan Temelkovski Dr. Tamas Kiss Dr. Gabor Terstyanszky University of Westminster.](https://reader030.fdocuments.in/reader030/viewer/2022033100/56649d765503460f94a57618/html5/thumbnails/1.jpg)
Extending a molecular docking tool to run simulations on clouds
Damjan TemelkovskiDr. Tamas Kiss
Dr. Gabor Terstyanszky
University of Westminster
![Page 2: Extending a molecular docking tool to run simulations on clouds Damjan Temelkovski Dr. Tamas Kiss Dr. Gabor Terstyanszky University of Westminster.](https://reader030.fdocuments.in/reader030/viewer/2022033100/56649d765503460f94a57618/html5/thumbnails/2.jpg)
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
![Page 3: Extending a molecular docking tool to run simulations on clouds Damjan Temelkovski Dr. Tamas Kiss Dr. Gabor Terstyanszky University of Westminster.](https://reader030.fdocuments.in/reader030/viewer/2022033100/56649d765503460f94a57618/html5/thumbnails/3.jpg)
Virtual Screening Reverse Docking
L1
L2
L3
L4
L5
R1 L1
R2
R4
R3
R1
![Page 4: Extending a molecular docking tool to run simulations on clouds Damjan Temelkovski Dr. Tamas Kiss Dr. Gabor Terstyanszky University of Westminster.](https://reader030.fdocuments.in/reader030/viewer/2022033100/56649d765503460f94a57618/html5/thumbnails/4.jpg)
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
![Page 5: Extending a molecular docking tool to run simulations on clouds Damjan Temelkovski Dr. Tamas Kiss Dr. Gabor Terstyanszky University of Westminster.](https://reader030.fdocuments.in/reader030/viewer/2022033100/56649d765503460f94a57618/html5/thumbnails/5.jpg)
• 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
![Page 6: Extending a molecular docking tool to run simulations on clouds Damjan Temelkovski Dr. Tamas Kiss Dr. Gabor Terstyanszky University of Westminster.](https://reader030.fdocuments.in/reader030/viewer/2022033100/56649d765503460f94a57618/html5/thumbnails/6.jpg)
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
![Page 7: Extending a molecular docking tool to run simulations on clouds Damjan Temelkovski Dr. Tamas Kiss Dr. Gabor Terstyanszky University of Westminster.](https://reader030.fdocuments.in/reader030/viewer/2022033100/56649d765503460f94a57618/html5/thumbnails/7.jpg)
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
![Page 8: Extending a molecular docking tool to run simulations on clouds Damjan Temelkovski Dr. Tamas Kiss Dr. Gabor Terstyanszky University of Westminster.](https://reader030.fdocuments.in/reader030/viewer/2022033100/56649d765503460f94a57618/html5/thumbnails/8.jpg)
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
![Page 9: Extending a molecular docking tool to run simulations on clouds Damjan Temelkovski Dr. Tamas Kiss Dr. Gabor Terstyanszky University of Westminster.](https://reader030.fdocuments.in/reader030/viewer/2022033100/56649d765503460f94a57618/html5/thumbnails/9.jpg)
Questions
?