Grid-enabled Virtual Screening Against Malaria

Abstract

WISDOM is an international initiative to enable a virtual screening pipeline on a Grid infrastructure. Its first attempt was to deploy large scale in silico docking on a public Grid infrastructure. Protein-ligand docking is about computing the binding energy of a protein target to a library of potential drugs using a scoring algorithm. Previous deployments were either limited to one cluster, to Grids of clusters in the tightly protected environment of a pharmaceutical laboratory or to desktop Grids. The first large scale docking experiment ran on the EGEE Grid production service against targets relevant to research on malaria and saw over 41 million compounds docked for the equivalent of 80 years of CPU time. Up to 1,700 computers were simultaneously used in 15 countries around the world. Issues related to the deployment and the monitoring of the in silico docking experiment as well as experience with Grid operation and services are reported in the paper. The main problem encountered for such a large scale deployment was the Grid infrastructure stability. Although the overall success rate was above 80%, a lot of monitoring and supervision was still required at the application level to resubmit the jobs that failed. But the experiment demonstrated how Grid infrastructures have a tremendous capacity to mobilize very large CPU resources for well targeted goals during a significant period of time. This success leads to a second computing challenge targeting avian flu neuraminidase N1.

High-Energy Physics Applications on the Grid

“…The a p plicatio n we u s e h e re a s a n exa m ple is High -Thro ug h p u t Scree ni ng in Dr ug Discovery. The firs t a p plicatio n in t his field is WISDOM [27] active o n t h e EGEE infra s t r uc t u re since 2 0 0 5. In 2 0 0 6, a n ew p h a s e was s t a r te d wit h t he ar rival of n ew collab o r a to r s (mos t n o t a bly by Aca de mia Sinica Taipei [28]) a n d wit h t he s t a r t of a s e t of ca m p aig n s agains t t he H5N1 vir u s (Bird Flu).…”

Bringing flexibility to virtual screening for enzymatic inhibitors on the grid

“…The commonly considered causes of error associated with distributed computing, such as power outages, routine resource maintenance, or disk errors [6], are out of the hands of the user in preventing delays in a virtual screening experiment. The scripts described in this paper manage job distribution by communicating with the Grid services hosted on the remote clusters and checking job status.…”

“…Grid computing has been shown to be a well-suited environment for implementing molecular docking software to perform virtual screening experiments in a number of studies [5][6][7]. The distributed nature of the Grid allows performing the virtual screening process as a large number of individual computational experiments in parallel, with performance increasing linearly with the number of CPUs in use [8].…”

CodeCloud: A platform to enable execution of programming models on the Clouds

“…Organizations started sharing computational power and storage (among other resources) in the so-called Grids, where scientific users could execute large experiments. Grid computing has proved to be a valuable tool not only to foster collaboration among research but also to aggregate enough computing power to tackle challenging problems that could not have been solved before [1].…”