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LigandFit explained | Project
FAQ | Project
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Cancer Project FAQs
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How do I know you will
actually do useful and scientifically valid computations on my computer? |
United Devices is working on this project with the University of Oxford, the
National Foundation for Cancer Research, all highly visible, well-respected
organizations. Please feel free to review the web sites of each of these
organizations to confirm their involvement.
In addition, our members can see the project themselves via the UD Agent
interface. UD is committed to Member involvement — Members will always have
information about the project that their machines are working on.
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What is contained in the
files I send back to the United Devices servers? |
Each result set contains the 3D molecular structures and corresponding scores
generated during the screening process. This data is important in the result
post-processing phase of the cancer project.
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How many conformations
does each molecule go through? |
Each molecule is different, and the number of conformations differs molecule to
molecule. Some molecules may be more complex, or have more flexibility, and thus
will have more conformations.
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Why does the conformer
counter reset every so often? |
When LigandFit has completed analysis on one molecule and has started another,
the conformer count begins again.
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What's the difference
between a conformer and a de novo structure? |
Conformers are molecules with the same molecular structure (same number of atoms
and same atoms are bonded within the molecule) but with a different 3-Dimension
representation due to twisting of various internal bonds. A de novo structure,
or de novo derivative, is a molecule that has actually been altered slightly
rather than just contorted.
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My Task Execution
Progress bar is frozen at a particular percentage. When I close the UD
Agent and restart it, it stays at that percentage but I lose some time.
Is the UD Agent frozen? |
Currently, the checkpoints in LigandFit are set after every successfully
completed molecule. If you turn off your PC, or restart the UD Agent, you may be
stopping it from completing the current molecule. When you restart it is going
back to the beginning of that complex molecule. This is why it seems you are
losing time. We are working on a fix, but in the meantime try allowing the UD
Agent to run for a longer period.
It's likely that the LigandFit task is not stuck. The % indicator is not a
linear time indicator; it counts the percentage of molecules in the work unit
that have completed processing. The reason that the time on the task bar
continues to increment even though the % counter stays the same is that the UD
Agent is still doing matches with the protein and the same molecule.
The time it takes to process a work unit varies depending on the Members'
system and the molecules' complexity. All molecules are different. Some
molecules may take a few moments to be processed by the UD Agent, while others
can take several minutes, or even hours depending on the speed of the machine.
Since the % indicator increments by molecule, it will stay the same for long
periods as the UD Agent works through these more complex molecules.
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Why does the protein
look so different from the molecule? Where are the atoms and/or bonds in
the protein? |
There may be thousands of atoms in any one of the target proteins; it often
makes sense to visualize the complete protein structure using
"space-fill" representations.
In comparison to one of our target proteins containing some 3000+ atoms, an
example drug-like molecule being considered may consist of a mere 20-50 atoms
— imagine how tiny the drug-like molecule would be if we displayed it on
screen using the same scale as that for the protein!
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Why don't some of the
molecules look like real and/or viable molecular structures? |
It's difficult to pick the best viewing angle with which to view these molecules
on the screen. It is not uncommon to have a view of a molecule that hides its
most interesting structural features. At present, there is no means for a person
viewing LigandFit's task graphics to control the 3-D orientation of a molecule
on screen, but United Devices is investigating the possibility for the future.
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Can I choose which
molecules or proteins that I want to work on? |
No, these are organized to best perform and track the research. The system does
not allow for selection of research components.
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Why does the UD Agent
sometimes display a blank molecule in the LigandFit application? |
Sometimes when the UD Agent or computer is restarted, LigandFit will not draw
the 3 dimensional representation of the molecule that it is working on. However,
the research will continue to function normally, incrementing the time on task.
When the UD Agent moves on to a new molecule, a graphic representation will
reappear.
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Can I combine efforts by
forming a team? If so, how? |
Yes, you may combine your efforts into a team. To learn how, visit the team area
of the United Devices Web site: http://www.grid.org/services/teams/.
Click on any team name to learn more about or to join the team. You can also
create your own team by scrolling to the bottom of the page and clicking on
'create a new team.'
More frequently
asked questions.
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