I have been using PyRx to dock peptides to a protein. Initially the numbers were small so it was okay. But now I have to dock over 500 peptides and doing so manually would take forever. My research partner is trying to dock with Galaxy but we are having difficulties. Is there an option for high throughput docking similar to PyRx?
Rad Shahmat
Have you tried using Autodock Vina? I have never used it for peptide-protein docking before but I use it for ligand-protein docking. You can also try to use this website I have found, I have also never used it before. Hope this helps. http://biocomp.chem.uw.edu.pl/CABSdock
I use PyRx which uses autodock vina for docking. It is integrated with PyRx. I tried to install autodock vina separately. But after installation, it does not open. Could I be doing something wrong?
Rad Shahmat Can you please add details on what error you get on pyrx???
Dr Thirumal Kumar D I am not getting any error on PyRx. In PyRx I can only dock one molecule at a time. I wanted to know if there is a way to dock multiple molecules one after another to make the workflow faster. I have over 500 molecules and docking all of them one by one manually would take a lot of time.
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