As a journalist at IDG Communications:
An international scientific collaboration has managed to whittle down the equivalent of 420 years of work on a single PC to no more than four months with the use of Grid computing.
The project, dubbed WISDOM (World-wide In Silico Docking On Malaria), ran between 1 October 2006 and 31 January 2007. With the use of computers from the EU-funded Enabling Grids for E-sciencE (EGEE) project, scientists were able to analyse an average of 80,000 drug compounds each hour, in search for a drug that will combat malaria.
As the name suggests, Grid computing is the linking of many individual resources, even down to desktop computers, to make a virtual supercomputing network.
Up to 5,000 computers were used at any one time, generating a total of 2,000GB of useful data. More than 140 million compounds were processed by the end of the four months, and results are expected to speed up and reduce the costs involved in searching for an anti-malaria drug.
"Drug development is a very long process, typically [lasting] 12 years and [costing] US$800 million," said Vincent Breton, a research associate at the French National Centre for Scientific Research who worked on the project. "What WISDOM shows is that the first step of this process which is drug discovery can be significantly accelerated and made cheaper using grids. This is particularly relevant to neglected diseases which suffer a lack of R&D."
Computers were connected using existing research network infrastructure and spanned 27 countries including the UK, France and Korea. All computers ran open source grid software, gLite, which allowed them to access central grid storage elements which were installed on Linux machines located in several countries worldwide.
Besides being collected and saved in storage elements, data was also analysed separately with meaningful results stored in a relational database. The database was installed on a separate Linux machine, to allow scientists to more easily analyse and select useful compounds.
"This shows how well Grids allow researchers to share resources," Breton said. "The UK computers [which contributed almost half the computing resources] used were mainly bought to run particle physics data analysis, but in their spare time are helping find new drugs. I can't imagine that this would happen without a Grid."
Using FlexX software developed at Germany's Fraunhofer Institute and donated by the BioSolveIT company, WISDOM used the EGEE Grid to match 3-dimensional structures of proteins from the malarial parasite to ligands, chemical compounds that bind to protein receptors.
"Grids are particularly well suited to drug discovery because you can compute the probability for one ligand to fit, or 'dock', to one protein on each computer node in the Grid, giving massive parallelism," Breton said.
It takes between a few seconds and a few minutes to model whether there's a match between a protein and a ligand. The 2006-2007 WISDOM project analysed more than 41 million compounds - the equivalent of 80 years' work on a single PC - in just six weeks.
