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.