Hi every one
I have a peptide library (around 300 peptides) that I would like to dock peptides to its target while I want a high throughput molecular docking webserver or software to do this. Does anyone know any web server or software for this purpose?
To perform molecular docking for a peptide library:
Dear Saegol
thanks for your answer. I could not be able to access Glide as its commercial tool. as I know Autdock is not suited for peptides. The peptide length in my library is more than 10 amino acids. could I use Autodock for peptides with this length?
Hello Ladan Mafakher,
I wouldn't use Autodock if you want to dock peptides longer than 10 residues, you may have more degrees of freedom than a small-rigid organic molecule, and you may not sample enough possible conformations of the peptide at your binding site. Better use Haddock:
https://wenmr.science.uu.nl/haddock2.4/
Bests,
thanks but I want to dock the library of peptides and HADDOCK could not do docking for multiple peptides in one run.
You may try the standalone version of HADDOCK then:
https://www.bonvinlab.org/software/haddock2.2/download/
Also, you may try FlexPepDock from Rosseta. Maybe that one is easier for running a whole library
https://www.rosettacommons.org/docs/latest/application_documentation/docking/flex-pep-dock
Bests,
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