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computer power. The rerei nement of 18,738 PDB i les with 18,738 inde-
pendent jobs requiring from 1 to 24 hours of CPU each is a very good
example of a parallel project ideally suitable for deployment on a
computing grid.
The rerei nements of the structure models were performed on a hybrid
computer environment consisting of the Biomed and EMBRACE [26] vir-
tual organizations on EGEE grid infrastructure as well as several clusters
of EMBRACE partners in Europe. Each grid job consisted of 20 proteins
that would run for 20 hours approximately on queues of 72 hours and
were managed using the WISDOM production environment. More than
90% of the total of 17 years of CPU time was i nished in two months. The
18,738 rerei nements were completed in four months. The rerei ned struc-
ture models are available from http://www.cmbi.ru.nl/pdb_redo/.
Selection of ligands can signii cantly reduce the number of compounds
docked. It can be based on the toxicity or on the properties of the target
binding site. We are presently investigating existing open-source software
packages to i lter the ligands before their docking on the grid.
Acknowledgments
The authors would like to acknowledge the contribution from numerous
collaborators to the research activities described in this chapter. We would
like to particularly thank Vincent Bloch, Ana Da Costa, Gianluca Degliesposti,
Matteo Diarena, Géraldine Fettahi, Nicolas Jacq, Yannick Legrè, Simon
Nowak, and Jean Salzemann.
The work described in this chapter was partly supported by grants from
the European Commission (BioinfoGRID, EGEE, Embrace), the French
Miinistry of Research (AGIR, GWENDIA), and the regional authorities
(Conseil Régional d'Auvergne, Conseil Général du Puy-de-Dôme, Conseil
Général de l'Allier).
The Enabling Grids for E-sciencE (EGEE) project is cofunded by the
European Commission under contract INFSO-RI-031688. The BioinfoGRID
project is cofunded by the European Commission under contract INFSO-
RI-026808. The EMBRACE project is cofunded by the European Commis-
sion under the thematic area “Life sciences, genomics and biotechnology
for health,” contract number LHSG-CT-2004-512092. The SHARE project is
cofunded by the European Commission under contract number FP6-2005-
IST-027694.
AuverGrid is a project funded by the Conseil Regional d'Auvergne.
The AGIR and GWENDIA projects are supported by the French Ministry
of Research.
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