Here is a recent description of the project, in general, from the UD FAQ:The United Devices Cancer Research Project will advance research to uncover new cancer drugs through the combination of chemistry, computers, specialized software, and organizations and individuals who are committed to fighting cancer.
The research centers on proteins that have been determined to be a possible target for cancer therapy. Through a process called "virtual screening", special analysis software will identify molecules that interact with these proteins, and will determine which of the molecular candidates has a high likelihood of being developed into a drug. The process is similar to finding the right key to open a special lock—by looking at millions upon millions of molecular keys.
This research is basically a search, and has several components. They include several proteins, hundreds of millions of molecules, a software program that analyzes chemical reactions, and a software platform that enables distributed computation.
The search revolves around several proteins that have been identified by previous studies to be a good target for cancer therapy. These proteins have specific areas, or "target sites" in their structural make-up where a drug-like molecule could connect with the protein to create a desired interaction.
Participants in the United Devices Cancer Research Project are sent a ligand library over the Internet. Their PC will analyze the molecules using a docking software called LigandFit by Accelrys. The LigandFit software analyzes the molecular data by using a three-dimensional model to attempt to interact with a protein binding site. When a ligand docks successfully with a protein the resulting interaction is scored and the interactions that generate the highest scores are recorded and filed for further evaluation.
Even with extensive pre-screening, the whittled-down number of molecules to review for this project is estimated at over two hundred million for each protein—a daunting number. Analyzing this quantity of anything requires an enormous amount of computational power. And when the numbers are this big, even supercomputing is limited. A super computer has a peak capacity. That is, if a workload is three times the capacity of the computer, the jobs must be "queued up" and attacked consecutively. A project like this one might take so much time that a researcher wouldn't even embark on it—he or she wouldn't see the end result in their lifetime. However, with distributed computing, thousands or even millions of individual computers can each work on different molecules simultaneously, and the time to results can be significantly lessened.
The screen shows a series of 3-dimensional images of molecules on the right. The molecules are made up of various elements, which appear as colored balls or rods. There are several primary elements that make up most biological molecules, which you can identify using the atomic legend on the screensaver.
The image at left of the screen represents one of the protein targets that the molecules may interact with. It is one of a series of targets that will be mapped against each of the potential drug molecules that are targeted for screening during this project.
What you will see is the molecule going through a virtual analysis, performing automated docking of flexible ligands to a protein's binding site.When a ligand docks successfully with a protein the resulting interaction is scored and the interactions that generate the highest scores are recorded and filed for further evaluation.
Other buttons on the graphic interface allow access to more information about the work the specific computer is doing, how it compares to other computers, and more project details.
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by Sir Joseph  edited by KeysCapt
last modified: 2003-05-11 20:15:17 |
