I would like to dock a short (12AA) peptide sequence to a few model inorganic surfaces.
It appears that similar simulations are being done by Jeff Gray's group with RosettaSurface, but its most recent implementation (and tutorial!) seem to be written for Rosetta 2.3...
A closer look at my installed version (3.4) reveals a surface_docking folder in /src/protocols/, but I cannot seem to find any corresponding executables.
Can anyone comment as to the availability and/or implementation of protein-surface docking in Rosetta 3.4?
The executable that runs surface_docking has not yet been released. I've let its authors (Michael Pacella, or maybe Robin Thottungal) know you're interested if they want to pass the executable part to you.
Posting this email here for future reference if anyone else is interested in obtaining a RosettaSurface executable. I'm happy to help!
My name is Mike Pacella, I am a graduate student in Jeff Gray's lab and a member of the RosettaCommons. Steven Lewis pointed me to your question on the RosettaCommons message boards and I wanted to reply to you personally on the status of the code. Surface docking has been ported to Rosetta 3 and, in preliminary tests, has been shown to reproduce results from Rosetta 2. However, I have not yet had the time to write up detailed documentation for the code and to ensure that it is up to the standards set by the RosettaCommons community, which is why the executable itself is not included in the Rosetta 3.4 release. If you would like, I can send you what documentation I have as well as an additional source code file that will allow you to re-compile and generate a surface_docking executable. Jeff only asks that you understand that this code is still in its testing phase and that the additional source code file I send you will still be the intellectual property of the RosettaCommons. Let me know and I'd be happy to send these materials to you and help you get started!