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

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