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1.1 General Info
This FAQ is about UD, a cancer-fighting project. The TSC (Juvenile Diseases) FAQ is here.
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Submitted by Jeffsul ... graphics added later.
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".
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.
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 rapidlythe 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!
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.
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 structuresor 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
You'll see a lot of discussion in the forum about "hits". Here is a brief explanation:
When a conformation docks successfully and triggers a positive interaction with the protein, it registers as a "hit". These hits are what this research hinges on. Any one hit may be the one that will ultimately lead to a cure. All hits are all recorded, ranked as to strength, and filed for the next stage of the project.
Do all proteins yield hits? The answer is No. Not all work units will produce hits - which is why we are doing this. If the scientists knew in advance exactly which protein target/molecule combinations would produce positive interactions we would not be here running this software.
So why are so many people concerned with hits? They don't add to WU points, and a no-hit WU result is just as valuable as a 700 hit WU result. But we're human, and we want to think that all that crunching is having some results, so we like to see those hits.
Just because a hit was found doesn't mean that molecule can be used - all the hit/no-hit molecules will be further studied to find why some have binding site preferences while similar molecules may not - what we're basically doing is the grunt work of classifying different molecule structures into hit/no-hit groups, the most time-consuming, calculation-intensive part of the research.
And once again, a completed WU with no hits is just as valuable as a WU with many hits.
This entry is a compilation of posts by Ian Brooks and MRK and was suggested by hockeyfun1 .
So what should I do?
Most of the team who have only one machine pick UD or TSC and run only one, while others switch back and forth between projects. If you chose to alternate projects, make sure you allow enough time on each one to complete the work unit currently being processed, especially with UD (since UD takes considerably more time to complete a work unit).
It shows our advances in the fight against cancer, and how we are helping.
To better understand what we contribute everyday, take a look at this 8 chapter video program at
Nova Online called Cancer Warrior.
*Requires: QuickTime | RealVideo
There are ONLY A FEW instances when it is feasible to run more than one project at a time. A fast dually system, plenty of RAM, and knowing that the work units will complete in the allotted time frame allowed is one example of that. More often than not neither project will benefit if both are struggling for CPU priority.