Dear researchers,
I need to draw relatively long peptide (40 residues) containing a non-amino acid linker as well as some organic radicals like fatty acid parts and others.
On the next step I will use the Macromolecule model to predict my peptide's 3D-structure. And finally I am going to run a protein-protein docking protocol to check interaction between my peptide and some receptors.
The last two steps seem fine, but I stuck with my hybrid peptide drawing.
It is quite easy to draw a simple peptide from a sequence, but how can I connect non-amino acid par to peptide?
I can build via "3D Builder" but it is quite tedious and annoying to draw organic radicals by hand.
2D-sketcher is not working for long peptides. Even when I drew a short peptide in 2D-sketcher and inserted it in a workspace the Schrodinger didn't recognize amino acid residues not allowing further work with peptide.
Could you please advise how to draw and prepare this kind of non-trivial peptide in Schrodinger?
Thank you!