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Protein Molecule Simulation in EDGeS

Protein Molecule Simulation in EDGeS. Tamas Kiss – University of Westminster Leader of the EDGeS Application Support Service E-mail: kisst@wmin.ac.uk. EDGeS Application Example Protein Molecule Simulation using AutoDock. Users and Use Cases

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Protein Molecule Simulation in EDGeS

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  1. Protein Molecule Simulation in EDGeS Tamas Kiss – University of WestminsterLeader of the EDGeS Application Support ServiceE-mail: kisst@wmin.ac.uk The EDGeS project receives Community research funding

  2. EDGeS Application Example Protein Molecule Simulation using AutoDock Users and Use Cases • Department of Molecular & Applied Biosciencesat UoW • Potentially large bioscience community using AutoDock • Extends a larger application scenario currently being investigated within the JISC ENGAGEProSim project.

  3. EDGeS Application Example Protein Molecule Simulation using AutoDock • AutoDock: • a suite of automated docking tools • designed to predict how small molecules, such as substrates or drug candidates, bind to a receptor of known 3D structure • one run of AutoDock finishes in a reasonable time on a single PC. However, thousands of scenarios have to be simulated and analysed to get stable and meaningful results. • AutoDock has to be run multiple times with the same input files but with random factors • Simulations runs are independent from each other – suitable for DG

  4. BOINC to EGEE bridge EDGeS Application Example 2Protein Molecule Simulation using AutoDock gUSE WS P-GRADE portal UoW Local Desktop Grid G-USE DG Submitter submits jobs and retrieve results via 3G Bridge BOINC Server Pulls work units Adds user credentials Submits as job to EGEE Define input parameters and number of work units WMS Workers: Download executable and input files Upload: result BOINC workers End User EGEE EDGeS VO

  5. EDGeS Application Example 2Protein Molecule Simulation using AutoDock UoW Local DG WS-PGRADE portal

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