Frequently Asked Questions about Metabolizer

Version 5.9.4

1. What is Metabolizer?
2. What is metabolite prediction good for?
3. Who uses Metabolizer?
4. Do you provide a GUI (graphical user interface) for Metabolizer?
5. Do I need programming skills to use Metabolizer?
6. How does Metabolizer work?
7. Do you provide a biotransformation library?
8. Can I change the behaviour of the biotransformations, for example their selectivities?
9. I am interested in bacterial (plant, rat, mouse, etc.) metabolism. Do you support that?
10. Can Metabolizer enumerate multiple generations metabolizing metabolites further?
11. How can I control how many metabolites are generated?
12. Can I export the metabolites to an SDfile?
13. I know the monoisotopic mass of metabolites from mass spectra. Can Metabolizer help me to find out what they are and how they were formed?
14. My compounds have metabolic stability problems, can I predict that?
15. I can enumerate plenty of metabolites in few generations, but I would prefer to see the major metabolites only. Can you predict major metabolites?
16. I need many generations of metabolites, but there is a risk to land in combinatorial explosion. How can I manage that?
17. What do you mean by a "major" metabolite?
18. What is production?

What is Metabolizer?

Metabolizer is an application of ChemAxon to enumerate xenobiotic metabolites of a given small molecule substrate.

What is metabolite prediction good for?

Metabolite prediction is useful to provide ideas about the metabolic fates of molecules. Metabolites may have biological effects that can be a risk for living organs.

Who uses Metabolizer?

Metabolizer can be used mostly by medicinal chemists, biochemists, biologists, toxicologists, environmental safety experts, bio- and cheminformaticians.

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

Yes, Metabolizer comes in the form of a desktop application, a command line interface and programming API.

Do I need programming skills to use Metabolizer?

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

How does Metabolizer work?

Metabolizer uses a biotransformation library containing generic "reactions" transforming the substrate to metabolites.

Do you provide a biotransformation library?

We are providing a small demo set of human phase one xenobiotic biotransformations at the moment, but we are developing the entire library of it.

Can I change the behaviour of the biotransformations, for example their selectivities?

Yes, you can edit all biotransformations.

I am interested in bacterial (plant, rat, mouse, etc.) metabolism. Do you support that?

Biotransformation libraries can be "plugged in". You can create your own biotransformation library. If you load it in Metabolizer, you will predict bacterial metabolites.

Can Metabolizer enumerate multiple generations metabolizing metabolites further?

Yes.

How can I control how many metabolites are generated?

You can modify the default limit of generations calculated, and there is a option to stop virtual metabolism of compounds by calculated proterties (i.e. number of atoms, logD).

Can I export the metabolites to an SDfile?

You can export the metabolites or a selected pathway to a wide range of chemical file formats including SDfile, SMILES, InChI.

I know the monoisotopic mass of metabolites from mass spectra. Can metabolizer help me to find out what they are and how they were formed?

Metabolizer displays the exact mass value for each metabolite.

Can Metabolizer predict the stability risk of a compound?

Yes, a well designed biotransformation library can estimate metabolic stability.

I can enumerate plenty of metabolites in few generations, but I would prefer to see the major metabolites only. Can you predict major metabolites?

Yes, Metabolizer predicts and highlights major metabolites if the used biotransformation library supports that.

I need many generations of metabolites, but there is a risk to land in combinatorial explosion. How can I manage that?

The major metabolic pathway method does not metabolize minor metabolites, so it helps to explore major metabolic pathways quickly.

What do you mean by a "major" metabolite?

Major metabolites are produced by fast biotransformations, but consumed slowly, so they accumulate.

What is production?

It indicates the relative amount of the substrate that is transformed to the given metabolite.