new variants leading to drug resistance.
One grid project is modelling the binding of 300?000 potential HIV protease inhibitors
© PHANTATOMIX / SCIENCE PHOTO LIBRARY
Arthur Olson, from the Department of Molecular Biology at The Scripps Research Institute in La Jolla, US, is using the World Community Grid to address this issue. 'From a medical point of view, evolution of resistance in HIV infected patients is a major threat to their continued survival. Our approach is to understand the mechanisms of viral resistance and to develop therapeutics that can box the virus into a corner from which it cannot escape.' The team is screening more than 300,000 molecules against multiple variations of two target sites on the HIV protease, which is involved with virus maturation. 'Typically we hope to whittle this number down to 30 or 40 compounds that we can then order and hand on to our collaborators to test experimentally,' he says.
Wide open possibilities
The future of research using the WCG isn't just about seeing how proteins interact with other molecules. At New York University, US, Richard Bonneau is using the WCG to predict how proteins fold. Taking the collection of microbes found inside and on the skin of humans, the team is looking at whether proteins derived from the genes of these organisms - many of which have gene sequences not seen before - perform novel functions or if their resulting protein structure is similar to known structures. 'Using the WCG, we can start to answer some of these questions and maybe uncover new enzymes or protein scaffolds while trying to understand the full extent of protein fold space,' says Kevin Drew, a doctoral student in Bonneau's team. Normally, this would be a costly and time consuming exercise but the WCG can help push findings into the lab, he says. To date, proteins translated from more than 94 genomes have been folded in this project.
Indeed, genomes and DNA are expected to play an expanding role in future grid research. Already, Olson and his team are beginning to use patient data to understand the individual variation in response to various HIV therapy regimes - a step, he says, towards more personalised treatments. Nakagawara agrees, saying the grid can be used for more personalised projects like genomics screening or signalling pathway analysis - both of which could play a role in next generation cancer treatments. 'The WCG can be applied to analyse the huge data sets obtained from DNA sequencing, transcriptome, proteomics and chemical structures to make personalised medicine possible.'
But this is just the tip of the iceberg when it comes to the grid's future research potential, says Jasinski. As long as the computational models are in place 'there is no real limit to the kinds of research areas the grid can contribute to'. Already the grid has been used to investigate environmental chemistry, how to produce more nutritious food and how to manage natural water courses for maximum benefit. But, says Jasinski, 'we also believe the grid can help in weather and climate models and in studies of topics in social sciences and humanities - such as comparative studies of literature, language, music. We are not limited to the physical sciences,' he says. 'We are only limited by the creativity of different research communities in their ability to create accurate computational models.' Idle or not, what better excuse is there to take that lunch break?
Katrina Megget is a freelance science writer based in London, UK
Community Computing - Idle Cures
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