Hello Orduz,

Here I have named two web based and freely available severs which run protein peptide docking. You have to provide protein structure (PDB ID) as target and peptide sequence of length (5-25 amino acids) as ligand.

1- CABS Dock

http://biocomp.chem.uw.edu.pl/CABSdock/

2- pepATTRACT

http://bioserv.rpbs.univ-paris-diderot.fr/services/pepATTRACT/

I found these software reliable. If you have Schrodinger software then you can use Peptide docking of Bioluminate.

If you have to design peptide library (like

overlapping peptide library,

Alanine Scanning Library Truncation Library Positional Scanning Library Random Library Scrambled Library T Cell Truncated Library) from specific sequences of proteins so you can use another web server named "Genescript"

https://www.genscript.com/peptide_screening_tools.html

You can also order peptides through it to perform experiment.

Very Thanks!

the first server Is in maintenance.

I will treat with the other. bioluminate is of full pay, the trial version contain this accessory?

yeah you can access through trial version. Peptide docking is the name of module in Bioluminate.

Pepfold is good one. You can try it!