Fragmenter
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Overview
Fragmenter uses RECAP and other methods to create building blocks by fragmenting larger molecules. Fragmenter is particularly relevant for generating analogues of biologically active compounds for lead discovery and for decomposing compounds to identify central structures.
Fragmenter also allows R-group decomposition of combinatorial libraries to determine substituents of a common scaffold to determine the key fragments responsible for high or low activity of an active compound family fragment statistics can be generated to identify the structure activity relationship
- Customizable fragmentation rules
- Built-in RECAP fragmentation module
- Built-in R-Group decomposition module
- Fragmentation information is stored with fragments
- Fragment statistics
This project was partially funded by the Hungarian National Office for Research and Technology under the contract number OMFB-00007/2006.
FAQ
What is Fragmenter?
Fragmenter is a toolkit of ChemAxon to break down input molecules to smaller pieces called fragments by cleaving bonds.
What is Fragmenter 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 I have to do programming for using Fragmenter?
No, programmability is just an option, you can use a simple command line interface.
What kind of additional software is needed?
Java version 1.5 or later.
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.
What is that CCQ fragmentation, how does it work?
The CCQ fragmentation method cleaves a carbon-carbon single bond next to a hetero atom.
Does CCQ open rings?
It opens aliphatic rings, but not aromatic ones.
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.
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.
