Metabolizer run vs. manual

Hi, I just started using metabolizer and I have a few questions:

I get different results when I select the molecule and press the run button or when I click on the + sign before the molecule manually, or double click the molecule. What is the difference? What is the influence of the set number of generations? Is it not the idea that you get more columns with more generations? When I press the run button I get a couple of metabolites in one column and they are all presented with 100% accumulation, what does this mean? 

Thanks a lot in advance,

Nadia

Hi Nadia,

Clicking the + sign means manual enumeration, enumerates the next generation of the selected compound, the Run button enumerate the given number of generations. There should be no difference however in the structures, so we will check if there is bug.

(The Run Major Pathways button produces less metabolites, the most likely ones only, speeding up the enumeration of large libraries.)

You can find some more details about the user interface here. Accumulation is a number indicating the likeliness/majority of a metabolite. You might see 100% when a the children of a metabolite are not enumerated yet. Here you can read some more about the calculation pro.

However, I would like to emphasize, that Metabolizer has not been released yet, just a preview is out for demo
purposes. It cannot be used for prediction at the moment, and due to the preview nature, it can contain some issues. We work on a human xenobiotic biotransformation library at the
moment which will fuel metabolizer with the necessary knowledge base
for prediction.

Gyuri

Thanks Gyuri for the fast reply,

when I press the run button, almost all compounds accumlute 100%. This is different from the manual results. I attache a print screen. Is this normal? What does it mean?

Nadia

Thank you, I could reproduce the issue, we try to figure out the source of it.

Hi Nadia,

 

Thank you for reporting this issue. The problem is found, and will be fixed soon - planned for the upcoming 5.6 or 5.6.1 release. The batch mode at the moment provides invalid results, that leads to bad accumulation data.

The "play" button should provide the same result as opening all nodes manually for N level.

 

Istvan Rabel

This has been fixed in the release version of Metabolizer.