Just like almost anything else related to computers, the United Devices project has a lot of jargon. We've defined a few terms below to help get you going.
 UD Agent Is the software you install.
United Devices is the name of the company that created and manages the UD Agent and related projects.
Work Units (WUs) or tasks: The UD Agent is a master program that is capable of running WUs or tasks for several different projects.
The Intel-United Devices Cancer Research Project is the molecular research project being conducted by the Department of Chemistry at the University of Oxford in England and the National Foundation for Cancer Research. It's being partially funded by Intel.
THINK is the task the UD Agent runs to carry out the work for the Intel-United Devices Cancer Research Project. But, for simplicity's sake, we just call it "UD".
Molecules
The UD Agent screen shows a series of images of 3-dimensional molecules on the left. The molecules are made up of various elements and bonds, which appear as colored balls put together with sticks. (The sticks represent the bonds between the elements.) There are several primary elements that make up biological molecules, which you can identify using the atomic legend on the screensaver. The other atom represented in the legend, called the hetro-atoms, signifies any different atom that isn't one of the usual five elements that make up most living matter. You can also see the numerical "molecular name" that each molecule has been given to track it.
Conformations
What you will see is the molecule going through a virtual analysis. It is contorted, or conformed, into a variety of different positions to attempt to map it to the protein target site. For example, a hydrogen atom may need to be closer to two oxygen atoms to potentially create an interaction. THINK will try to reshape the molecule in a variety of positions to get the elements together. Each reshaping of the molecules is a single conformation. THINK works through the molecules and each conformation very rapidly—the numbers move so fast that all the numbers representing each conformation on your screen do not appear, so only every few molecular conformations are visible on the screen. THINK is moving too fast to watch!
Proteins
The image at right 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 over two hundred million molecules that are targeted for screening for this project.
De Novo
Sometimes a molecule may have extra potential if it slightly altered in some way. When this is the case, THINK may consider mutations or substitutions to some conformers to produce de novo structures—or altered molecules.
The resulting new molecule's properties may be more desirable than the original. This process adds a few more variables to each molecular search so THINK can consider the most promising structures possible. Not all molecules will be structured in a way that is advantageous to alter, so the de novo counter will only appear intermittently.
Submitted by RClarkofNC
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by KeysCapt 
last modified: 2002-10-14 18:37:43 |
