3D 3 Point Descriptors

3D 3 Point Descriptors

The 3D 3 Point Descriptors are build from the 3 dimensional structure of the compounds each feature (pharmacophore) consists of 3 atoms with associated interaction eg. hydrogen bond acceptor, donor, hydrophobic, (pharmacophore point) and the distances between this features. Have a look at an example:

3D Pharmacophores pose quite a few challenges we have to deal with:

Depending on the completeness of the conformational analysis and the number of bins, which are used for the distances a compound will have many thousands of pharmacophores out of a list of a few millions. Some people are now using 4 and 5 point pharmacophores which allow to distinguish chiral elements but also greatly increase the number of pharmacophores.

Besides this problems 3D pharmacophores might have some advantages as compared to 2D descriptors, although the literature is controvers in real experimental results:

Currently WATER does not use 3D descriptors but the implementation does not pose any significant problem since conformational analysis algorithms are available on the marked from various sources.

Page Owner: Alberto Gobbi - Last updated: Apr 17, 1999