Is there a easy way to draw peptide structure

User 6ba4d9dd23

10-05-2013 04:31:07

Is there a easy way to draw peptide structure in instant jchem? For example, if I want to draw structure of Gln-Arg-Pro-Leu, do I have draw amino acid's structure one by one?

ChemAxon 2bdd02d1e5

10-05-2013 20:03:03

Hi,


yes, it should be possible to do this way if you allow empty structures on the table in schema editor(r-click on table -> Edit Data Tree). You can see it in the screenshot.


However then you have to query for structures only by using amino acids abbreviations. Searching by using full chemical structure will not retrieve structures written by abbreviations.


Cheers


Filip

User 6ba4d9dd23

10-05-2013 20:33:20










fzimandl wrote:

Hi,


yes, it should be possible to do this way if you allow empty structures on the table in schema editor(r-click on table -> Edit Data Tree). You can see it in the screenshot.


However then you have to query for structures only by using amino acids abbreviations. Searching by using full chemical structure will not retrieve structures written by abbreviations.


Cheers


Filip




Hi Filip,


Thank you for your help.


I already created a data tree which allows empty structures, but I do not know how to retrieve structures from amino acid abbreviations. Can you show me how to retrieve structures? Thanks.

ChemAxon 2bdd02d1e5

10-05-2013 23:37:55

I'm sorry, don't know it. Have to check it out if it will be possible by using standardizer. Thanks for your patience in the meantime.


Filip

ChemAxon 2bdd02d1e5

30-05-2013 10:11:02

Hi,


I'm sorry for the late answer, there were some problems with it and I originally thought it's will not be possible. Finally I have a solution for you. You must specify the standardizer on the entity. The stadardizer type for this use case is "Create Group". You can then setup the abbreaviation for related structure similarly as seen in screenshot.


For detailed manual about creating stadardizer read the tutorial at http://www.chemaxon.com/instantjchem/ijc_latest/docs/user/tutorials/Standardizer/htmlFiles/Standardizer.html.


Filip

User 6ba4d9dd23

01-06-2013 01:44:56

Hi Filip,


Thank you for your reply. I am still learning how to use standardizer. Do I have to use standardizer to convert peptide sequence, such as Glu-Asp-Ser-Glu, to structure? Is there a easier way ? Thanks.

ChemAxon 2bdd02d1e5

03-06-2013 13:59:17

No there is currently no other way in IJC. There are currectly some solutions in development, but I don't know the details, since it is not part of the Instant JChem development.

ChemAxon fa971619eb

11-06-2014 05:59:19

Actually there are ways. You can just paste an amino acid sequence into Marvin Sketch and it gets recognised. You can use 1 letter and 3 letter codes. Examples:
RGDP
Arg-Gly-Asp-Pro


Also, the amino acids are available as templates. Use the Insert->Templates menu item, and look at the amino acids section. A template can be added to the sketcher, and chains can easily be drawn (select the new amino acid from the template, click on the C-terminus of your current chain and drag out to the next position to extend the chain.


The amino acids are added as abbreviated groups. They can be expanded to show the full atom representation, or even ungrouped completely.


Tim