Rosetta@home - Computing Platform

Computing Platform

See also: List of distributed computing projects

Both the Rosetta@home application and the BOINC distributed computing platform are available for the Microsoft Windows, Linux and Macintosh platforms (BOINC also runs on several other platforms, e.g. FreeBSD). Participation in Rosetta@home requires a central processing unit (CPU) with a clock speed of at least 500 MHz, 200 megabytes of free disk space, 512 megabytes of physical memory, and Internet connectivity. As of May 24, 2012, the current version of the Rosetta application is 5.98, and the current version of the Rosetta Mini application is 3.31. The current recommended BOINC program version is 7.0.28. Standard HTTP (port 80) is used for communication between the user's BOINC client and the Rosetta@home servers at the University of Washington; HTTPS (port 443) is used during password exchange. Remote and local control of the BOINC client use port 31416 and port 1043, which might need to be specifically unblocked if they are behind a firewall. Workunits containing data on individual proteins are distributed from servers located in the Baker lab at the University of Washington to volunteers' computers, which then calculate a structure prediction for the assigned protein. To avoid duplicate structure predictions on a given protein, each workunit is initialized with a random number seed. This gives each prediction a unique trajectory of descent along the protein's energy landscape. Protein structure predictions from Rosetta@home are approximations of a global minimum in a given protein's energy landscape. That global minimum represents the most energetically favorable conformation of the protein, i.e. its native state.

A primary feature of the Rosetta@home graphical user interface (GUI) is a screensaver which shows a current workunit's progress during the simulated protein folding process. In the upper-left of the current screensaver, the target protein is shown adopting different shapes (conformations) in its search for the lowest energy structure. Depicted immediately to the right is the structure of the most recently accepted. On the upper right the lowest energy conformation of the current decoy is shown; below that is the true, or native, structure of the protein if it has already been determined. Three graphs are included in the screensaver. Near the middle, a graph for the accept model's free energy is displayed, which fluctuates as the accepted model changes. A graph of the accepted model's root mean square deviation (RMSD), which measures how structurally similar the accepted model is to the native model, is shown far right. On the right of the accepted energy graph and below the RMSD graph, the results from these two functions are used to produce an energy vs. RMSD plot as the model is progressively refined.

Like all BOINC projects, Rosetta@home runs in the background of the user's computer using idle computer power, either at or before logging into an account on the host operating system. Rosetta@home frees resources from the CPU as they are required by other applications so that normal computer usage is unaffected. To minimize power consumption or heat production from a computer running at sustained capacity, the maximum percentage of CPU resources that Rosetta@home is allowed to use can be specified through a user's account preferences. The times of day during which Rosetta@home is allowed to do work can also be adjusted, along with many other preferences, through a user's account settings.

Rosetta, the software that runs on the Rosetta@home network, was rewritten in C++ to allow easier development than that offered by its original version, which was written in Fortran. This new version is object-oriented, and was released on February 8, 2008. Development of the Rosetta code is done by Rosetta Commons. The software is freely licensed to the academic community and available to pharmaceutical companies for a fee.