The scripts and input files that accompany this demo can be found in the
demos/public directory of the Rosetta weekly releases.
KEYWORDS: SURFACES DOCKING
This demo will describe how to run the C++ version of the RosettaSurface algorithm. The test case shown here will analyze the adsorption of the model peptide LK-alpha to the 104 surface of calcite
Simultaneous optimization of protein rigid-body orientation, backbone and side chain conformations on a solid surface.
$> $ROSETTA3/bin/surface_docking.default.linuxgccrelease @rosetta_inputs/flags
In the above, ".default.linuxgccrelease" may need to be updated for your build, operating system, and compiler.
Ensure that the input pdb is properly formatted with the protein appearing before the surface in the input file and belonging to a separate chain
Ensure that the specified surface vectors match the input surface
Ensure that parameter files corresponding to the molecules comprising the surface exist in the rosetta database
Make sure that the folder contains either only adsorbed state PDBs (and native.pdb) or solution state PDBs. Also make sure that all post processing scripts (found in the scripts/post_processing directory) are present in this directory as well
These commands will extract the top 4 adsorbed-state decoys for analysis and generate secondary structure, protein-protein contact maps, and protein-surface contact maps
This app requires a single protein positioned above a solid surface whose parameters are present in Rosetta. The protein needs to appear before the surface in the pdb file and the two need to be separate chains