Where is Metabolizer?

User 9cc9c09363

12-01-2012 10:31:18

Hi. again.


I believed that metabolizer is in the package of JChem 5.7.1.


But after installation, I couldn't find one.. here I attached the capture of my windows showing the chemaxon programed installed in my computer..


Please confirm this and let me know..

ChemAxon d76e6e95eb

12-01-2012 10:39:54

A preview of Metabolizer was installed in previous versions, it contained a small demo biotransformation set and a substrate for demo purposes only. This preview has been removed from the installer since Metabolizer is "under construction" at the moment, its first official release will be out soon including a human biotransformation library.

User 9cc9c09363

12-01-2012 12:29:27

Thank you for your kind reply.


Where can I download the previous version of JChem including metabolizer?


I just want to check how it works and if it is possible to use this program for the purpose of my study.


Actually, the research I am doing is to predict the transformation products by chemical oxidation process.


we have many data for the reaction rules and kinetic information to put in the software.


Although metalbolizer was developed for biotransformation products I guess it would be also possible to apply this software to my purpose on the whole.


How do you think about this? Can the metabolizer include kinetic information?


 


Thank you for your support.


 

ChemAxon d76e6e95eb

12-01-2012 13:09:08

You can download earlier versions via the download page. Please see the jchem archive here. Metabolizer has not been released yet (just the preview was shown), so you should not rely much on the current API.


It does not handle kinetics, but it provides a way to set a kind of priority value (see the SPEED_CATEGORY property) for each generic biotransformation allowing to influence the prediction of major metabolites. You can create your own biotransformation library as well. Metabolizer is a tool to convert the given substrates according to a library of biotransformations, so Metabolizer is a conversion tool and the prediction capabilities depend on the library provided.

User 9cc9c09363

12-01-2012 14:27:28

Thank you very much!


I just installed the metabolizer and checked out.. as it is preview version, it looks limited..


Maybe last quenstion this time.. when will the metabolizer be released??


 

ChemAxon d76e6e95eb

12-01-2012 14:58:06

In few months time (I hope). Until that you might want to see the Reactor tool, actually, Metabolizer uses the same engine internally, maybe you can use that directly.

User 9cc9c09363

12-01-2012 15:46:17

Thank you very much for your kind reply. I really appreciate it.


As far as I understand the reactor, it provides only one step reaction.


In other words, It doesn't show me all tranformation products formed over the whole reaction because reactor can process only one reaction to give product at one time.


if I have this reaction, A=>B=>C=>D=>E, even though I can define each reaction step in reactor.


I can't combine all reactions together because I can only peak one reaction. (e.g., A=>B, or D=>E)


Maybe I am misunderstanding reactor.. Is there a way in reactor to put all reactions pathways together so that when I put reactants I can see all the transformation products possible by the rules I defined?


Once again thank you very much


 


 


 


 

ChemAxon d76e6e95eb

12-01-2012 15:50:01

Yest, that is true, Reactor can help if you are OK with some coding using the Reactor API. In this case you might initialize one Reactor object for each of your generic biotransformations and then call them in loops.

User 9cc9c09363

12-01-2012 15:59:21

Your answer is amazingly fast.. thank you so much.!


I see. maybe I can give it a try to do some coding.. but I have not any knowledge about code or something like that at all..


Do you have any maual regarding how I can initialize one reactor object and call them in the loops ?


 


Thank you.


 


 

ChemAxon d76e6e95eb

12-01-2012 16:33:02

You can find some basic guidelines in the apidoc, but you will certainly need some general coding experience to start with that.


Anyway, what features do you expect from a metabolite enumeration/prediction tool? With what would you be happy with? Your opinion is appreciated.

User 9cc9c09363

12-01-2012 17:06:15

Thank you for the answer.


Simply what I expect from using the your prediction tool is to predict the transformation products as accurate as possible and I will compare the simulated results with the experimental results for the compounds the transformation products of which both are elucidated and not.


Since I am dealing with chemical oxidation and many kinetic data are available, reaction results (e.g. concentration after certain reaction time) can be accurately predicted. so it would be great to be able to introduce this kinetic concept (rate constants and equilibrium constants and so on) in the prediction results. but I guess this is beyond the scope of both Metabolizer and code modified Reactor for the moment.. maybe you could work on this later in the future.


This study is just at beginning.. so I will face many problems soon and I might ask you many questions in the near future..


If you have any suggestion or advide, please let me know.


 


Thank you for all the answers you gave.


 

ChemAxon d76e6e95eb

13-01-2012 12:30:47

Yes, that is beyond the current scope of Metabolizer but sounds very interesting. If you land in troubles with the API, just open a new topic in this forum.