Similarity of Small Molecules Based on Three-Dimensional Structure

SIMILARITY OF SMALL MOLECULES BASED ON THREE-DIMENSIONAL STRUCTURE 

Precise definitions are needed if one is to use a program to recognize three-dimensional similarity. In this section we will discuss a variety of such definitions. Additionally, we will show how such definitions are used to recognize the proposed three-dimensional features that are common to a set of molecules, an especially important problem with structurally complex natural produas. 

It is important to distinguish between those three-dimensional properties of a molecule that relate purely to intramolecular relationships, geometric properties, from those three-dimensional properties that relate to the docking or superposition of a molecule with some other molecule, steric properties. Geometric properties do not change as the molecule is moved in space or for 

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PSSC is a knowledge-based approach to develop small-molecule inhibitors of protein function. Protein domains or cores with similar three-dimensional structures are clustered in so-called PSSCs. Knowledge about known ligands for members of such a cluster can be employed to guide the design of focused compound collections for screening on the other cluster members. Increased hit rates can be expected using this approach. 

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