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DDG

Delta Delta G (DDG) is a metric for predicting how a single point mutation will affect protein stability. DDG, often referred to as đš«đš«G, is the change in the change in Gibbs free energy (double changes intended). DDG is a measure of the change in energy between the...

Replace Ligand

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...

Selectors

Create a New Selector Edit an Existing Selector Apply a Selector Delete a Selector Rename a Selector How to Create a New Selector: Load a structure into CAD Click the residue(s) that you wish to select NOTE: Command is equivalent to Control on Windows Command (⌘) +...

Relax

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...

Minimize

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....

Structure Loader

Click on , which will open a new tab in the center window. Load a structure into CAD by either entering the PDB number into the space , then clicking the plus OR by clicking  to load a structure from your computer. Loaded files will be listed in the order they are...

Repack

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...

Prepare

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...