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GWG
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New Algorithm to help proteome folding?

This quote comes from the “ACM TechNews; Friday, March 9, 2007” email letter:

Novel Search Engine Matches Molecules in a Flash New Scientist (03/01/07) Knight, Will

Oxford University researchers have developed a way to match molecules of the same shape using the relative position of the atoms in a given molecule, an innovation that could be used to identify potential drugs very quickly. Similar shaped molecules are likely to have similar bioactive effects, causing a smaller medicinal effect in the human body. The 3D shape of a molecule is currently found by superimposing it over another molecule and measuring how much it overlaps, but this new technique, known as Ultrafast Shape Recognition (USR), maps and stores the relative position of atoms in the molecule, creating an accurate mathematical picture of its shape. The system allows molecules to be compared quickly and without concern for orientation in the database, which could prove extremely valuable given the billions of molecules currently contained in many databases. The technology could also be applied elsewhere. "Being able to match 3D objects is an important problem that might become even more important as we get more and more 3D models of our world--such as Google earth," says Carnegie Mellon image analysis expert Luis von Ahn. However, Imperial College molecular analysis expert Henry Rzepa says "part of the problem is that too little 3D shape information in a usable form actually exists. Even for molecules, proper 3D coordinates which define these shapes are all too rare."


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It is quite possible that the persons responsible for the design of the algorithms are already on to this, but if not, it occurs to me that searching a map of existing shapes and finding a close match would provide a better initial guess for shape on which to apply relaxation techniques to produce an improved shape simulation.
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retsof
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Re: New Algorithm to help proteome folding?

The research here attempts to define the shape of these protein molecules by folding and docking, since the shape isn't already known.
We can't use what we don't have.

Another observation is that Oxford already runs some projects on grid.org. I don't know whether this algorithm will be used in some way over there or not. It could be implemented in a future project to interact with KNOWN SHAPED MOLECULES. Grid helped out with the first phase of folding.
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Re: New Algorithm to help proteome folding?

Sounds like it could help with analyzing the results when we predict shapes using HPF2. It is the sort of tool that could be useful when working with our database of predicted shapes (structures).
[Mar 13, 2007 6:27:32 PM]   Link   Report threatening or abusive post: please login first  Go to top 
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