Thursday, March 19, 2009

Another Plug

There was a question that was posed as to the importance of the work that was being done in neuroblastoma with the World Community Grid. I realized that while I understood the importance of the target proteins they were trying to hit, I did not necessarily understand how all of the pieces fit together. This gave me an excuse to do a little research and another opportunity to get in another plug for this project. Remember, you can sign up here:
There is actually a great description of why this work is so valuable on the About page for the project. I have provided it below so that you can see how incredibly cool and important the work your computer is doing.
It has been demonstrated repeatedly that the function of a protein molecule - a substance made up of many atoms – is related to its three-dimensional shape. Scientists are able to determine by experiment the shapes of a protein and of a drug separately, but not always for the two together. If scientists knew how a drug molecule interacts with a target protein, chemists could design even better drugs that would be more potent than existing drugs.

To that end, the project's researchers are using computational methods to identify new candidate drugs that have the right shape and chemical characteristics to block three proteins - TrkB, ALK and SCxx, which are expressed at high levels or abnormally mutated in aggressive neuroblastomas. If these proteins are disabled, scientists believe there should be a high cure rate using chemotherapy.

The researchers have prepared a library of three million compounds - or potential drug candidates (called ligands) - and will use World Community Grid to simulate laboratory experiments to test which of these compounds block these proteins. Simulations will be conducted using Autodock, a suite of tools that predict how large numbers of different small drug molecules might bind to TrkB, ALK and SCxx, so the best molecules can be found computationally, before they are selected and tested in the laboratory for efficacy against neuroblastoma.

In the absence of World Community Grid, researchers would have to undertake their investigation through individual docking simulations, which would take approximately 8,000 years to complete. With World Community Grid, analysis can be carried out for thousands of drug candidates in parallel, allowing high throughput screening to be conducted. Researchers estimate this will reduce the time required to about 2 years.

This added level of speed and sophistication could potentially enable researchers to identify new drug candidates for neuroblastoma, thereby facilitating discovery of prognostic clues, which are not apparent by human inspection or traditional analysis alone and could advance the fields of cancer biology, drug discovery and therapy planning.
See, I told you your computer could have purpose.

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