Toward a 3D Search Engine

Plasma Droid writes "NewScientistTech has a story about a 3D molecular search engine that is over 1,500 times faster than anything previously developed. The researchers, from Oxford University, developed a lightning-fast way to quickly match 3D shapes mathematically. This could not only speed up searches for new drugs, but lead to 3D search engines, for finding objects uploaded to platforms such as Google Earth, they say." The problem will be in jump-starting the supply of 3D data about molecules and everything else.

Comments

Enter Search Term:

[LiquidCoooled]

Boobies, extra large please.

Shape versus negative space

[goombah99]

It's pretty easy to geometrically hash or construct reduced feature vectors for matching. People (like me) have been doing this for years. It's much harder to know if a molecule will fit into a crevice or negative space. THe latter is probably more important to drug design. the reduced feature vectors let you know quickly if two molecules are simmmilar in shape. Which is the title given to the article. But then this is discussed in the context of drug targets. A harder problem. What maybe new or clever here is that they found a very useful set of feature vectors.

Re:Shape versus negative space

[Anonymous Coward]

It's pretty easy to geometrically hash or construct reduced feature vectors for matching. People (like me) have been doing this for years

I bet you have to beat the chicks away with a stick.

Re:WOO HOO!

[Kenja]

Hot molecule on molecule action! See uncensored carbon bonding!

Impact on Pharma (esp. patents)

[Mateo_LeFou]

I've always been of two minds about whether the drug industry was a good example of patents being cost-effective, because I suspect that very good technology will soon emerge that makes pharma R&D less expensive, by making it primarily a data-processing (esp. simulation) issue. Seems like this tech might be the first piece of that puzzle?

Good, but just one tiny bit of the problem

[filthWisard]

This is a really cool advance when working with molecules you already know the shape of, but it still doesn't get around the problem of what shape a molecule is in the first place. A protein molecule will naturally collapse into the shape with the lowest energy. If there are 100 atoms in the main chain, that's 99 different angles that it could have, that's 99 degrees of freedom. I hear that genetic algorithms are pretty good at finding the most lightly shape though, so this may not be as big a problem as it used to be.

Not enought structures?

[ajax142]

The author lists an apparent problem of this 3D search as a lack of molecular structures and calls for a "jump start" in the supply of 3D data, I call BS on this claim. A quick look at the Cambridge Structural Database shows 400,977 strucutures of 363,931 different molecules. There are another 89,064 structures of inorganic molecules in the Inorganic Crystal Structure Database. On the biological side there are 3,425 structures of Nucleic Acids in the NDB as well as 42,082 structures of proteins and polypeptides in the PDB. If that still isn't enough for the authors, fire up any number of ab initio quantum chemistry programs and in a short time you can create a library of good guesses for the structure of small molecules.

I tend to think the authors of the article are refering to the problems of a "useable form" for the structures and easy access of many of these databases. The first problem is mearly a problem of converting between the various structural file formats out there, something a good programmer (or grad student) can solve is a few weeks or less. The second is a bureaucrat issue and not a scientific one.