Hi Olanrewaju,

do you know the follwing two programs ?:

http://openbabel.org/wiki/Main_Page

http://bioware.ucd.ie/~cyclops/cgi-bin/webpep.cgi

Regards

Markus

Thank you so much @Marcus.

Also, I'll love to know if it is just ideal for peptides to fail druglikeness tests woefully cos the results I'm getting are alarming.

Thank you.

Dear Olanrewaju, dear Marcus

Option for translation peptide sequences into SMILES code has recently been added in the BIOPEP-UWM database (formerly BIOPEP)

http://www.uwm.edu.pl/biochemia/index.php/pl/biopep

Click "Boactive peptides" tab, then "Analysis" tab and then "SMILES" icon.

Paste your sequence into the window and click the icon "Show SMILES".

The application accepts L-Amino acids (annotated using capital letters: A, F, G), D-amino acids (annotated as a, f, g respectively) and phsphoserine (annotated as B or b for L- and D-enantiomer respectively).

We used algorithm, which may be considered as simplified version of CHUCKLES, similar to this used in CycloPs program. Set of SMILES strings of amino acids is compiled form CycloPs source codes, available in Github: (https://github.com/fergaljd/cyclops) and SwissSidechain database (https://swisssidechain.ch/).

All representations are verified and corrected according to recommendations from the following publication: Minkiewicz P., Iwaniak A., Darewicz M., 2017, Annotation of peptide structures using SMILES and other chemical codes–practical solutions. Molecules, 22, Article No 2075 (https://www.researchgate.net/publication/321315131_Annotation_of_Peptide_Structures_Using_SMILES_and_Other_Chemical_Codes-Practical_Solutions)

I hope that publication describes all relevant details of algorithm and verification.

You can compare BIOPEP-UWM with the CycloPs and OpenBabel using procedures described in the above publication.

The application translates only linear peptides without modifications. Disulfide bond and other modifications may be inserted using molecule editors.

Thanks a lot @ Piotr. That was also helpful.

I have found another opportunity for construction of SMILES representations of peptides.

Authors of publication linked below:

Article Novel Angiotensin-Converting Enzyme Inhibitory Peptides Deri...

Article Novel Angiotensin-Converting Enzyme Inhibitory Peptides Deri...

Recommend ChemSketch program for construction of SMILES representations of peptides. This program may be downlowade here:

https://chemsketch.en.softonic.com/download

I can add, that MravinSketch (ChemAxon, Budapest, Hungary) may be used for construction of SMILES strings of peptides. The program provides opportunity to import of SMILES strings of amino acids, connect them into peptides and export again as peptide SMILES string.

It can be done with the appropriate version of ChemDraw, which is commercial software:

http://informatics.perkinelmer.com/Support/KnowledgeBase/details/Default?TechNote=673

Basically you type a sequence into a text box (HGluGlyOH is given as example in the link), generate the structure using the 'Expand Label' command, and use the Edit->Copy As->SMILES command to get the SMILES string.

There is another program generating SMILES strings of peptides. Porogram Dendrimer Builder, provided by Prof. J. L. Reymond's group at University of Bern, Switzerland is available via the following address:

http://dendrimerbuilder.gdb.tools/.

It is designed for construction of representations of branched peptides.

I have just found one more program sufficient for construction of SMILES strings of peptides. It is molecule editor of NANPDB database:

http://african-compounds.org/nanpdb/compounds_structure/