I am using RosettaLigand design protocol to design protein binders for a small molecule. The tutorial I referred to is Mr. Rocco Moretti's paper ( Methods Mol Biol. 2016 ; 1414: 47–62. doi:10.1007/978-1-4939-3569-7_4.).
According to the tutorial, "the provided protocol only does one round of design and minimization. Additional rounds may be desired for further refinement. Simply replicate the low_res_dock, design_interface, and high_res_dock lines in the PROTOCOLS section to add additional rounds of design and optimization."
I am not sure if it's correct to write like this, two runs for example.
Any suggestion will be appreciated!
You have the general sense of it. One thing you may want to try, though, is to add a designinterface step between the middle high_res_dock and low_res_dock pairs. This will allow Rosetta to better capitalize on that intermediate high res docking step, by allowing it to refine the protein sequence for the structure that's found by high res docking.
Hello, sir. I think I get it. Thanks a lot for your suggestions!