define new aminoacids

hi people:





Well, I have a peptide sequence with a modification in one of the aminoacids (Serine) and I want to convert this peptides to a smile format. To do this, I need the definition of the Serine in Smarts format, and with this, define a new Serine with the modification. In the picture attached bellow I show the problem. Well, the questions is :





How can I defined the modification of the new aminoacid in marts fomat as a custom aminoacid for (SERINE (S),Trionine(T), Tyrosine (Y))?





Where are the file with the definitions of aminoacids in the Jchem Instalation?





Thanks in advance





Yasset.

Dear Yasset,





Peptide definitions can't be modified yet, so if you want to modifiy a peptide, you have to do it manually after import.





The easiest way to do it, to define a custom template in the mskecth, and then, you can change the default group to this by one click.

With chemaxon we should defined new aminoacids as:





  X(Hcy)    X(Hcy)      [SX2H1][CH2][CH2][C@HH1]([NX3])C=O    5     6





  X(1-foo)   X(1-foo)    [SX2H1][CH2][C@HH1]([NX3])C=O          4      5


X(b) X(b) [CH3][CH2][CH2][CH2][CH2][C@HH1]([NX3])C=O 7 8


(This example is from the documentation)











Well a need to defined my need aminoacids as a modification of the (SERINE (S),Trionine(T), Tyrosine (Y)). Then I need the standard SMARTS definition of these aminoacids to re-defined with a modification. My idea is to add a phophorilatyion modification to OH group.

Yes, you can define a new aminoacid, but can't modify the original one.





So, you can create a new peptide, with the given format. eg.:





X(Sph)    X(Sph)    [#7][C@@H](COP(O)([#8-])=O)[C]=O    1    9











To use it, you need to put it into the the custom_aminoacids.dict file. If you have no custom peptide definitions yet, this file doesn't exist, so you need to create it to your chemaxon home directory. (This is .chemaxon (UNIX) or chemaxon directory in user's home (MS Windows).)





I hope, could help





Suti

Thanks for all:





   I need the original definitions only for a guide to re-defined in a new file named custom_aminoacids.dict. I don't know the definition in SMARTs format the (SERINE (S),Trionine(T), Tyrosine (Y)) and for these reason I need the definition from chemaxon original file. I try with the option convert from peptide sequence to SMARTs but it don't work.





Thanks in advance.

The original dictionary is attached. (Format is the same, as the custom dictionary.)





How did you tried to convert the peptides to SMARTS?





Kind regards,


Suti

Hi Suti:





Finally I defined my custom_aminoacids.dict file in the chemaxon directory (attach below). But when I run the command





            molconvert smiles lolo.seq -o lolo.smi 





the program show me the error :





chemaxon.formats.MolFormatException: Could not find aminacid in peptide string H-S-K-K-K-K-S-X(SerP)-T-T-K-OH


        at chemaxon.marvin.io.formats.peptide.PeptideReader.convert(PeptideReader.java:127)


        at chemaxon.marvin.io.formats.peptide.PeptideImport.readMol(PeptideImport.java:102)


        at chemaxon.marvin.io.MRecordImporter.readDoc(MRecordImporter.java:170)


        at chemaxon.formats.MolImporter.readDoc(MolImporter.java:702)


        at chemaxon.formats.MolConverter.readDoc(MolConverter.java:792)


        at chemaxon.formats.MolConverter.convert0(MolConverter.java:706)


        at chemaxon.formats.MolConverter.convert(MolConverter.java:658)


        at chemaxon.formats.MolConverter.main(MolConverter.java:1517)


lolo.seq:1: error: SKKKKSX(SerP)TTK : error in molecule file





The file lolo.seq contain sequence SKKKKSX(SerP)TTK





Thanks in advance.

This is a problem with the converter, and will be fixed at next release.





The first letter inside X(...) must be uppercased, the other letters must be lowercased.


So, if you change X(SerP) to X(Serp), it will work.





Thanks for report.

Hi Suti:





   Thanks for all, finally the program convert sequences to smiles format. But the definition is wrong because   the new peptides are in wrong form.  





I think that the error is in the index of the:

1. the number of the backbone N in the SMARTS string (the third atom
   
   
   for Ala in the first line of the example)




2. the number of the backbone C next to the acyl oxygen (fourth atom
   
   
   for Ala in the first line of example).

My idea is obtain a SERINE (S),Trionine(T), Tyrosine (Y)) in a phosphorilatyon form. My definition is attached in the previous post as a custom_aminoacids.dict file.





You might check the file?





Thanks for all.

The SMARTS of your peptides must be correct, but the attachpoints you defined are not represents the same atom as at the original peptides.


If I am right, you want to keep the attachpoints. In this case, I think the correct atomnumbers are:





X(Serp)    X(Serp)    [NX3][C@@H]([CH2]OP(O)([#8-])=O)C=O    1       9


X(Thrp)    X(Thrp)    [CH3][C@@H](OP(O)([#8-])=O)[C@H]([N;X3])C=O    9       10


X(Tyrp)    X(Tyrp)    [NX3][C@@H]([CH2]C1=[CH1][CH1]=C(OP(O)([#8-])=O)[CH1]=[CH1]1)C=O    1       15





(The atoms contains to the attachpoints shown bold.)





Kind regards,





Suti

Thakns for all Suti..