WISDOM: A Grid-Enabled Drug Discovery Initiative against Malaria - Grid Computing: Infrastructure, Service, and Applications - page 353

Finally, grids provide the resources to speed up the execution of time-
consuming software:

• in silico drug discovery,

data analysis and mathematical modeling
The application of high-performance computing to new areas

Access to large computing resources for

•

• The production of additional or more accurate analyses

• The facilitation of the exchange of tools and workl ows between

scientists
The performance of computing intense tasks in a transparent way •

by means of an automated job submission and distribution facility
Access to services and resources 24 hours a day •

• The running of the same job on many platforms across different

sites
Access to computing resources by a single efi cient path •

Grids are unique tools for collecting and sharing information, network-
ing experts, and mobilizing resources routinely or in an emergency. A grid
is thus an appropriate environment to develop in silico drug discovery.

14.2.2 Grid-Enabled Virtual Screening

Virtual screening is about selecting in silico the best candidate drugs act-
ing on a given target protein [2]. Screening can be done in vitro but it is
very expensive as there are now millions of chemicals that can be synthe-
sized [3]. A reliable way of in silico screening could reduce the number of
molecules required for in vitro and then in vivo testing from a few millions
to a few hundreds. Docking is only the i rst step of virtual screening since
the docking output data have to be processed further [4].
However, in silico virtual screening requires intensive computing, in the
order of a few TFlops per day, to compute 1 million docking probabilities
or for the molecular modeling of 1000 compounds on one target protein.
Access to very large computing resources is therefore needed for success-
ful high-throughput virtual screening [5].

14.2.2.1 The Virtual Screening Pipeline

Screening of chemical compounds against a target is an important step in
the drug discovery process. Virtual screening is the process that screens
the chemical compounds in silico against a target. The prerequisite to set
up a virtual screening experiment is knowledge on the target, against
which the screening has to be performed, and on the chemical compound
libraries. Most of the information related to the targets is available in the
literature, whether it is digital or paper based.