Preparing for the Workshop
UNIX Operating Systems
Workshop activities will be conducted on provided computers running Linux. It is expected that participants will have basic familiarity with the operation of the Linux command line.
Many resources for learning the Linux command line are available online. Here are some suggestions to get you started
- University of Surrey Unix Terminal Tutorials: Contains workable examples. Highly recommended.
- Linux Command: Learning the Shell
Scripting Languages
Rosetta users often prepare input files and analyze Rosetta output models using scripts typically written in Python. While the workshop does not require the knowledge of scripting langauges, understanding the provided scripts and troubleshooting them is easier if you have familiarized yourself with Python:
Molecular Visualization Tools
You will also need a tool to visualize biomolecular structures. We will assume the use of PyMOL, but you can use any of the tools below:
Rosetta Resources
You can learn more about Rosetta using these resources:
The tutorials are based in part on on the following papers:
- Kaufmann, K. W., Lemmon, G. H., Deluca, S. L., Sheehan, J. H., & Meiler, J. (2010). Practically useful: what the Rosetta protein modeling suite can do for you. Biochemistry, 49(14), 2987-2998.
- Bender BJ, Cisneros A, Duran AM, Finn JA, Fu D, Lokits AD, Mueller BK, Sangha AK, Sauer MF, Sevy AM, Sliwoski G, Sheehan JH, DiMaio F, Meiler J, & Moretti R. (2016). Protocols for Molecular Modeling with Rosetta3 and RosettaScripts. Biochemistry, 55(34), 4748-63.
- Schoeder CT, Schmitz S, Adolf-Bryfogle J, Sevy AM, Finn JA, Sauer MF, Bozhanova NG, Mueller BK, Sangha AK, Bonet J, Sheehan JH, Kuenze G, Marlow B, Smith ST, Woods H, Bender BJ, Martina CE, Del Alamo D, Kodali P, Gulsevin A, Schief WR, Correia BE, Crowe JE Jr, Meiler J, Moretti R (2021). Modeling Immunity with Rosetta: Methods for Antibody and Antigen Design Biochemistry, 60(11):, 825-846.
Materials from previous workshops can be downloaded from the Meiler Lab website.
Additional demos can be found on the RosettaCommons website.