I try to find where is the binding sites of peptide (7 amino acid) on enzyme. And I run Plexpepdock (Rosetta 3.4) . I do not have any informations and the binding site and the backbone of peptide (I just have the sequence).
The fisrt time, I try to move peptide on cleft manually and chose the structure have lowest score. But, I think this is not a good way to cover all the cleft of enzyme by peptide.
Do you know any command line I need to add on the flags which can help peptide move or if any programe can generate coordinates of peptide automatically which can cover cleft better.
Thank you so much
I m waiting your reply.