Comparison of 2D similarity and 3D superposition. Application to searching a conformational drug database.

In a database of about 2000 approved drugs, represented by 10(5) structural conformers, we have performed 2D comparisons (Tanimoto coefficients) and 3D superpositions. For one class of drugs the correlation between structural resemblance and similar action was analyzed in detail. In general Tanimoto coefficients and 3D scores give similar results, but we find that 2D similarity measures neglect important structural/funtional features.

Accelerating screening of 3D protein data with a graph theoretical approach.

Motivation: The Dictionary of Interfaces in Proteins (DIP) is a database collecting the 3D structure of interacting parts of proteins that are called patches. It serves as a repository, in which patches similar to given query patches can be found. The computation of the similarity of two patches is time consuming and traversing the entire DIP requires some hours.