The scripts and input files that accompany this demo can be found in the
demos/public directory of the Rosetta weekly releases.
KEYWORDS: STRUCTURE_PREDICTION GENERAL
This demo contains the starting structure for the original published use of FloppyTail, and is a copy of FloppyTail's integration test. To run the demo (in the inputs subfolder):
$> cd inputs $> $ROSETTA3/FloppyTail.linuxclangrelease @options
Read the options file first to set local paths as needed.
Please refer to FloppyTail's documentation (in the online manual, or in your copy of the code at Rosetta/documentation/application_documentation/structure_prediction/floppy-tail.md, and its publication Kleiger G, Saha A, Lewis S, Kuhlman B, Deshaies RJ. Rapid E2-E3 assembly and disassembly enable processive ubiquitylation of cullin-RING ubiquitin ligase substrates. Cell. 2009 Nov 25;139(5):957-68. PubMed PMID: 19945379. Note that the paper is primarily about biology, not modeling.
Note that the provided outputs are from the integration test, which runs in ~30 s. You will need to run FloppyTail for much longer (both longer individual runs, and many trajectories) to get scientifically useful results. The options file and documentation provide details on how to do that.