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.

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Speed versus Thoroughness

[wsherman]

NewScientistTech has a story about a 3D molecular search engine that is over 1,500 times faster than anything previously developed.

The implication both from the summary and from the article itself is that this new search is just as thorough as other search methods but much faster. To prove thoroughness they would have had to show that anything found by other search methods will also be found by their new, much faster, search method. I doubt very much that they were able to do prove this rigorously.

That's not to say that the problem of matching 3D molecular shapes is not important or that their research is not valuable. I would say, though, that it is misleading to claim that they have solved the 3D search problem with a much faster algorithm. There are many different measure of 3D similarity and, for many measures of similarity, the only way to guarantee an optimum match is by exhaustive search.

Note that, in general, every search will be exhaustive in the sense that the query must be compared to every entry in the database. The problem is that many measures of similarity have additional parameters that must be optimized by exhaustive enumeration for each comparison. The classic example is a measure of 3D similarity that pairs each atom in the query with an atom from the structure in the database. In the general case, all possible pairings must be tried through an exhaustive enumeration.

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.