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more accurate modeling tools before biological tests are undertaken.
Molecular dynamics (MD) [13] has great potential at this stage: i rst, it
enables a l exible treatment of the compound/target complexes at room
temperature for a given simulation time, and therefore is able to rei ne
compound orientations by i nding more stable complexes; second, it
partially solves conformation and orientation search dei ciencies that
might arise from docking; third, it allows the reranking of molecules
based on more accurate scoring functions.
Just at the time when the results of the i rst WISDOM data challenge were
being analyzed at SCAI Fraunhofer by Vinod Kasam, the BioinfoGRID proj-
ect was launched in January 2006. LPC Clermont-Ferrand contribution to
the project focused on the deployment of MD computations on the grid.
14.3.3.2
Deployment
Work started on the identii cation of the relevant molecular dynamics
software and on the choice of the grid infrastructure on which to deploy
the computations. Contacts were established with two groups at SCAI
Fraunhofer and University of Modena, which expressed interest in rerank-
ing the best hits coming out of the i rst WISDOM data challenge. Both
groups were using the Amber software for molecular modeling which
raised again the problem of deploying a licensed software on a grid.
Contacts were established with the institution distributing Amber regard-
ing the license policy on the grid.
The outcome of the negotiation was that we were allowed to deploy
Amber on the grid under the following conditions:
•
Each cluster deploying Amber had to have at least one license.
•
Grid users allowed to use Amber had to come from one of the
laboratories owning an Amber license.
Grid users allowed to use Amber under the conditions described
•
above could deploy their computations on all the grid clusters.
Regarding the choice of infrastructure, contacts were established with the
EGEE biomedical virtual organization and several groups involved in
DEISA. A clear preference for deployment on EGEE was expressed by the
groups collaborating with us at the University of Modena and SCAI
Fraunhofer. Both had developed MD procedures that were well i tted for
running on clusters. As a consequence, we focused our efforts on deploy-
ing these procedures on EGEE.
From September 2006, we started to investigate in detail the deployment
of the MD procedure designed by Giulio Rastelli (University of Modena
and Reggio Emilia) on EGEE and based on the Amber software package.
Amber [14] is a suite of different tools that carry out molecular dynamics
simulations. The simulations in Amber can be divided into three phases
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