convert structure <-> sequence

Dear support,





I would like to convert a peptid sequence into a structure or convert a peptid structure into its sequence. Is there a way to do that with the API and/or a bat file?





Thank you very much,


Severine

Dear Severine,





From Marvin 4.1 we (will) support importing and exporting peptide sequences. Marvin 4.1 alpha release can be downloaded from http://www.chemaxon.com/shared/alpha/. You can import 1-letter or 3-letter peptide sequences to MarvinSketch by opening the file which contains the sequence. After opening the file the peptide is shown as a sequence of abbreviated groups. You can select the structure and ungroup it to get a "regular" chemical structure (see image below). Exporting a structure to sequence works only if the peptide is represented as a sequence of abbreviated groups each being an amino acid (the sequence must start with H- at and end with -OH).





An API example for converting peptide sequence to SDfile:

Code:

import java.io.IOException; import chemaxon.struc.*; import chemaxon.formats.MolImporter; public class PeptideToSDF {     public static void main(String[] args) {         Molecule mol;         try {             MolImporter mi = new MolImporter(args[0]);             mol = mi.read();             mol.ungroupSgroups(); // not needed if converting to smiles             System.out.print(mol.toFormat("sdf"));         } catch (IOException e) {             // TODO Auto-generated catch block             e.printStackTrace();         }     } }

I have attached this example as PeptideToSDF.java. After compiling it can be used like this:

Code:

java PeptideToSDF peptide.seq > peptide.sdf

peptide.seq is the file containing the peptide sequence (can be 1-letter or 3-letter) and peptide.sdf is the generated output file.





You can also use Standardizer ( http://www.chemaxon.com/jchem/doc/user/Standardizer.html ) to convert a peptide sequence into a structure :

Code:

standardize peptide.seq -c ungrup.xml -f sdf > peptide.sdf

I have attached the ungrup.xml file.





Note: all described methods work only with Marvin 4.1 release!





Best regards,


Zsolt

Thank you Zsolt.





I will try it and tell you in case of problem but I think there will not be.





Severine

Hello, if you are storing large peptides in sdf file format it is worth to double-check the original documentation on the format http://www.mdli.com/downloads/public/ctfile/ctfile.jsp since it is not intended for big biopolymers (ie with more than 255 atoms/bonds).