by Elizabeth Swanberg | May 21, 2019 | Actions, Tools
NOTE: An error message will appear if one or more CA…CA distances are detected to be too far apart in your structure after you click ‘Save and Run’. You will get this error if the distance in the starting coordinates for the loop you are attempting...
by Elizabeth Swanberg | May 16, 2019 | Actions, Tools
OVERVIEW Restrain Ligands is an option that can be activated during Repack, Minimize, Loop Rebuild, or Design. This is intended to freeze the molecule in place in relation to the protein during modeling. Warning: Only turn this on if you want the ligand to stay in...
by Elizabeth Swanberg | Dec 31, 2018 | Actions, Tools
OVERVIEW The Replace Ligand tool allows you to swap a new ligand into a pocket in place of an existing ligand. This is useful when you want to dock a molecule that is similar to a ligand with a known binding conformation. Design and other modeling can then be carried...
by Elizabeth Swanberg | Dec 18, 2018 | Actions, Tools
INTRODUCTION Many design tools have been developed by Rosetta labs and the three most refined methods have been incorporated into Cyrus CAD for easy use. These tools (Design, Flex Design, and Relax Design ) have been well-tested in the Rosetta labs where they were...
by Elizabeth Swanberg | Dec 16, 2018 | Actions, Tools
Relax is one of the most used Rosetta methods for sampling conformational changes in a protein. It is more aggressive than Minimize, so it tries out orientations that are up to a few angstroms away from the starting structure. RUNNING RELAX Select the folder that...
by Elizabeth Swanberg | Dec 16, 2018 | Actions, Tools
Minimize is a quick way to find the optimal conformation of your protein in the near vicinity of the structure’s current orientation. This will find the local energetic minima, but not the global minima. It is often used as a last step during structure optimization....
by Elizabeth Swanberg | Dec 16, 2018 | Actions, Tools
OVERVIEW Repack will sample side chain orientations while keeping the backbone fixed in order to find an energetic minima. Running Repack will affect the entire protein. This can be individually by clicking Repack, but is also done during all other Actions that...
by Elizabeth Swanberg | Dec 16, 2018 | Actions, Tools
Prepare runs the Relax protocol, which aggressively minimizes backbone and side chain, while placing very tight constraints on every heavy (non-hydrogen) atom to keep the structure very close to the original crystal structure. So this is more restrained that a normal...
