Frequently Asked Questions about Fragmenter

Version 5.9.4

1. What is Fragmenter?
2. What are fragments good for?
3. Who uses Fragmenter?
4. Do you provide a GUI (graphical user interface) for Fragmenter?
5. Do I need programming skills to use Fragmenter?
6. What fragmentation methods are currently supported by Fragmenter?
7. How does transformation-based fragmentation work?
8. Do you support RECAP fragmentation?
9. The transformations change the functional groups, is there a way to "remember" the original functional groups?
10. Does Fragmenter cleave bonds in all permutations?
11. Does the transform-based fragmentation open rings?
12. Can I avoid generation of small fragments?
13. What is that CCQ fragmentation, how does it work?
14. What other configuration options are available for CCQ fragmentation?
15. Does CCQ open rings?
16. How are connection points labelled in case of CCQ?
17. How do you compare the transfomation-based cleaning method to CCQ, which is the recommended one?

What is Fragmenter?

Fragmenter is a toolkit of ChemAxon to break down input molecules to smaller pieces called fragments by cleaving bonds.

What are fragments good for?

Fragments can be used as building blocks in some drug design methods (i.e. random evolutionary drug design), or used as indicators of a certain biological effect (i.e. activity or toxicity analysis).

Who uses Fragmenter?

The primary users of Fragmenter are drug designers, medicinal chemists, toxicologists and cheminformaticians.

Do you provide a GUI (graphical user interface) for Fragmenter?

Not at the moment, we provide a command line interface and programming API.

Do I need programming skills to use Fragmenter?

No, programmability is just an option, you can use a simple command line interface.

What fragmentation methods are currently supported by Fragmenter?

Two fragmentation methods are available at the moment. One is based on given transformations, the other (CCQ) uses a simple rule.

How does transformation-based fragmentation work?

You provide a set of transformations describing how to cleave certain functional groups in the form of reaction schemes (SMIRK, RXN). Then fragmenter will cleave the input molecules using those transformations.

Do you support RECAP fragmentation?

We provide a basic RECAP transformation set, that you can use immediately.

The transformations change the functional groups, is there a way to "remember" the original functional groups?

Yes, the connection points are labelled according to the original functional group (like amide nitrogen).

Does Fragmenter cleave bonds in all combinations?

Yes.

Does the transform-based fragmentation open rings?

It would not yield smaller fragments, so there is an option to avoid ring opening.

Can I avoid generation of small fragments?

Yes, there is an option to limit the size of the generated fragments.

What is that CCQ fragmentation, how does it work?

The CCQ fragmentation method cleaves a carbon-carbon single bond next to a hetero atom.

What other configuration options are available for CCQ fragmentation?

Nothing is needed. The simple CCQ cleavage rule does not change functional groups, it does not open aromatic rings, does not cleave hetero atoms from rings. Very simple and effective.

Does CCQ open rings?

It opens aliphatic rings, but not aromatic ones.

How are connection points labelled in case of CCQ?

No labels are needed for maintaining the original functional group information as they remain intact. However, if you fragment molecules containing explicit hydrogens only, connection points are marked with implicit hydrogens in the fragments.

How do you compare the transfomation-based cleaning method to CCQ, which is the recommended one?

The transfomation-based method (i.e. RECAP) is customizable by transforms and options, you can greatly influence which bonds are cleaved. The CCQ method is traditionally used for building block generation. CCQ has one simple rule, it is extremely fast and can be used for toxicophore generation as it does not modify the functional groups.