Forum for Science, Industry and Business

Sponsored by:     3M 
Search our Site:

 

Networking computers to help combat disease

24.01.2006


3D structure of a target protein from Plasmodium falciparum (Credit: SCAI Fraunhofer)


3D-representation of a ligand (red) inside proteins from Plasmodium falciparum (blue – yellow) (Credit: SCAI Fraunhofer)


Subtropical diseases lay waste to millions of people each year. In the quest to find a cure scientists are using Grid computing, the major driving force for new approaches towards collaborative large-scale science, to discover new drugs and better understand the diseases.

Last year there were about 350-500 million infections and approximately 1.3 million deaths due to malaria, mainly in the tropics. Malaria is spread by female mosquitoes, which carry protozoan parasites called Plasmodium.

Currently drug discovery seeks compounds that can inhibit or kill invading parasites and infections, but there are potentially millions of candidate compounds. It can take 10 years to discover a drug and another 10 to get it approved.



Grid technology, where the resources of many computers in a network are applied to a single problem at the same time can reduce candidate compounds from millions to thousands or even hundreds, isolating the most promising candidates and speeding up the discovery process.

The new research is particularly important because these diseases are comparatively neglected by large pharmaceutical companies. "The idea for malaria came from a conversation I had with a friend, a pastor who works in Burkino-Faso, who told me that malaria is the biggest problem faced by the country," says Dr Vincent Breton, Research Associate at France’s Corpuscular Physics Laboratory (CNRS-IN2P3).

"Quite often it’s just the developed world that benefits from high-technology like Grid computing. I wanted Grids to benefit Africa," says Breton.

Two European projects are currently searching for candidate treatments, the Enabling Grids for E-sciencE (EGEE) project-based Wide In Silico Docking on Malaria (WISDOM), and Swiss Bio Grid’s DENGUE project. This type of research contrasts with in vitro and in vivo approaches and is now a hugely important first step in large-scale biological analyses.

Using the FlexX software developed at the 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," says Breton.

It takes between a few seconds and a few minutes to model whether there’s a match between a protein and a ligand, and the WISDOM project performed the equivalent of 80 CPU-years of calculations in just six weeks.

Analysis of WISDOM results at Germany’s Fraunhofer Institute for Algorithms and Scientific Computing (SCAI), joint instigators and participants of the project alongside France’s CNRS-IN2P3, allowed the 1,000 most promising compounds out of 1 million candidates to be selected using a relative ranking scale between different ligands. The project identified both known candidates and new ones, which demonstrated the validity of the approach.

"Now we will use a supercomputer to even more precisely model the match between the candidate ligands and the proteins," says Breton.

Refined docking requires intensive computation because researchers must account for molecular dynamics. "There are a lot of atoms and we want to model how they interact with each other to further refine the ranking order of candidate compounds," says Breton. Grid computing works excellently for computation of large data sets that can be broken down into discrete tasks, while supercomputers excel at modelling highly interconnected data sets.

Drug discovery is probably the most exciting use of Grid technology in the battle against disease, but it is not the only one. The Africa@home project allows people to donate idle CPU cycles in a distributed infrastructure to perform epidemiological modelling. This enables researchers to calculate the impact of vaccines, for example, or the spread of a disease.

"But that’s not the only way to use Grids in epidemiology," says Breton. "They could also be used to federate databases collecting data on infection and treatment in malaria and Dengue, but also in HIV. This is vitally important information that is currently very difficult to collect in Africa."

"This project shows the importance of Grid technology, and the value of a resource like EGEE," concludes Breton.

Tara Morris | alfa
Further information:
http://istresults.cordis.lu/index.cfm/section/news/tpl/article/BrowsingType/Features/ID/80155

More articles from Information Technology:

nachricht Five developments for improved data exploitation
19.04.2017 | Deutsches Forschungszentrum für Künstliche Intelligenz GmbH, DFKI

nachricht Smart Manual Workstations Deliver More Flexible Production
04.04.2017 | Deutsches Forschungszentrum für Künstliche Intelligenz GmbH, DFKI

All articles from Information Technology >>>

The most recent press releases about innovation >>>

Die letzten 5 Focus-News des innovations-reports im Überblick:

Im Focus: Making lightweight construction suitable for series production

More and more automobile companies are focusing on body parts made of carbon fiber reinforced plastics (CFRP). However, manufacturing and repair costs must be further reduced in order to make CFRP more economical in use. Together with the Volkswagen AG and five other partners in the project HolQueSt 3D, the Laser Zentrum Hannover e.V. (LZH) has developed laser processes for the automatic trimming, drilling and repair of three-dimensional components.

Automated manufacturing processes are the basis for ultimately establishing the series production of CFRP components. In the project HolQueSt 3D, the LZH has...

Im Focus: Wonder material? Novel nanotube structure strengthens thin films for flexible electronics

Reflecting the structure of composites found in nature and the ancient world, researchers at the University of Illinois at Urbana-Champaign have synthesized thin carbon nanotube (CNT) textiles that exhibit both high electrical conductivity and a level of toughness that is about fifty times higher than copper films, currently used in electronics.

"The structural robustness of thin metal films has significant importance for the reliable operation of smart skin and flexible electronics including...

Im Focus: Deep inside Galaxy M87

The nearby, giant radio galaxy M87 hosts a supermassive black hole (BH) and is well-known for its bright jet dominating the spectrum over ten orders of magnitude in frequency. Due to its proximity, jet prominence, and the large black hole mass, M87 is the best laboratory for investigating the formation, acceleration, and collimation of relativistic jets. A research team led by Silke Britzen from the Max Planck Institute for Radio Astronomy in Bonn, Germany, has found strong indication for turbulent processes connecting the accretion disk and the jet of that galaxy providing insights into the longstanding problem of the origin of astrophysical jets.

Supermassive black holes form some of the most enigmatic phenomena in astrophysics. Their enormous energy output is supposed to be generated by the...

Im Focus: A Quantum Low Pass for Photons

Physicists in Garching observe novel quantum effect that limits the number of emitted photons.

The probability to find a certain number of photons inside a laser pulse usually corresponds to a classical distribution of independent events, the so-called...

Im Focus: Microprocessors based on a layer of just three atoms

Microprocessors based on atomically thin materials hold the promise of the evolution of traditional processors as well as new applications in the field of flexible electronics. Now, a TU Wien research team led by Thomas Müller has made a breakthrough in this field as part of an ongoing research project.

Two-dimensional materials, or 2D materials for short, are extremely versatile, although – or often more precisely because – they are made up of just one or a...

All Focus news of the innovation-report >>>

Anzeige

Anzeige

Event News

Expert meeting “Health Business Connect” will connect international medical technology companies

20.04.2017 | Event News

Wenn der Computer das Gehirn austrickst

18.04.2017 | Event News

7th International Conference on Crystalline Silicon Photovoltaics in Freiburg on April 3-5, 2017

03.04.2017 | Event News

 
Latest News

NASA's Fermi catches gamma-ray flashes from tropical storms

25.04.2017 | Physics and Astronomy

Researchers invent process to make sustainable rubber, plastics

25.04.2017 | Materials Sciences

Transfecting cells gently – the LZH presents a GNOME prototype at the Labvolution 2017

25.04.2017 | Life Sciences

VideoLinks
B2B-VideoLinks
More VideoLinks >>>