Speaker
Describe the scientific/technical community and the scientific/technical activity using (planning to use) the EGEE infrastructure. A high-level description is needed (neither a detailed specialist report nor a list of references).
Docking is the method of first choice for rapid in silico
screening of large ligand
databases for drug research, since it is based on a rational
physical model and very
fast. Thus, in 2005 during the first WIDSOM data challenge this
method has been
employed to screen the ZINC database for compounds potentially
inhibiting the Malaria
parasite plasmodium falciparum by blocking one of its particular
proteases. As a
result, guanidinium compounds, so far not known to inhibit the
tested plasmepsin hav
With a forward look to future evolution, discuss the issues you have encountered (or that you expect) in using the EGEE infrastructure. Wherever possible, point out the experience limitations (both in terms of existing services or missing functionality)
We will present and first results generated during WISDOM2 for
demonstrating both,
the benefits as well as the limits of the chosen approach. We
will discuss also the
problems encountered with experiments, where a DAG Job,
controlled by WMS starts
hundreds of follow up jobs automatically over many days and the
dependencies on the
stability of the resources. It is of interest to run the
Moleculardynamik part of the
workflow on DEISA. We are in discussion with FzJ to use it as Demo.
Describe the added value of the Grid for the scientific/technical activity you (plan to) do on the Grid. This should include the scale of the activity and of the potential user community and the relevance for other scientific or business applications
Drug design for neglected deseases is adressed in the WISDOMI and
II.
The docking process is now combined with Moleculardynamics, which
is heavy computing
intensive and may be provide more accurate results.
Report on the experience (or the proposed activity). It would be very important to mention key services which are essential for the success of your activity on the EGEE infrastructure.
Therefore, a workflow combining the docking program FlexX2,3 and
parts of the
molecular dynamics (MD) package AMBER 84 has been set up. Since
MD calculations tend
to become quite consumptive, the workflow has been implemented
using the
EGEE-middleware gLite5 for performing world wide large scale
studies in order to
rerank the hits of the previous simple docking experiment. With
the invention of the
Workload Management Service gLite is able to handle so-called DAG
(Directed Acyclic
Graphs) jobs. Our directly with gLite features deployed workflow
consist of 15 stages
were each stage consist of subjobs and the number of subjobs
depend on the size of
the input. No portal and no workflow engine is used.
Each stage executes the different programs like FlexX, Amber etc.
Data is held on the
storage elements and Metadata is stored in database.
