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Scaffolds and Frameworks

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Table of Contents

1. Definition  -  
2. Scaffold report  -   analyse scaffold diversity, and the most populated scaffolds

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Definition - top

When a new molecule is imported in a database, two types of substructure will be computed and associated with it: the scaffold and the framework. The scaffold retains all rings and linkers between rings, and removes all lateral chains, with the exception of exocyclic double bonds. The Framework of a molecule is the same as the scaffold, except that atom types are removed, bond orders are set to 1, leaving all atoms to SP3 carbons. The only exception here is 6-membered aromatic rings, for which the bond order is kept to retain aromaticity.

Scaffolds and frameworks are computed by the Molecular Handler. If you are not happy with the current definition, and you know JAVA programming, you can provide your own implementation by changing the handler which is associated with your own database. Then you will have to recalculate all scaffolds in your database using the top menu bar:
Database->Admin->Recalculate scaffolds and frameworks

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Scaffold report - top

The scaffold report lets you analyse the most populated scaffolds, and compute various indices that give you insight into the scaffold diversity of your database.

Let's give an example, using the Demo database (that you can create by checking the appropriate checkbox in the Create database wizzard, or by following the quickstart guide).

Compute a scaffold report on the whole database Compute->Scaffolds - Frameworks->Scaffolds report. As you may have noticed, you can compute the same report for frameworks, and for a specific library instead of the entire database. You should end up with the following window:

Here you have a set of indices that will give you insight into the scaffold diversity of your database (or library). I will not enter into too much detail about them, because as you can see, there are a magic button associated with each indice, which will popup a help window describing the value.

On the second tab, you will see the top 100 most populated scaffolds in your database.

For each scaffold, the number of molecules associated with it is given as a label located under the molecule (number in brackets). 20 scaffolds are represented in each page using the left and right arrows in the toolbar. You can also save all these scaffolds in a sdf file.

Finally, you can select one or several scaffold by clicking on it's label (it will be highlighted in red), and perform usual actions on the molecules associated with these scaffolds, e.g. saving them as a new library ...

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