  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 pervasive grids. The first large scale docking
experiment ran on the EGEE grid production service from 11 July 2005 to 19
August 2005 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.
