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 | Rosetta
Overview An Energy Function is one of the most important tools for modeling a molecular structure. It provides a way to determine if a structure is favorable compared to alternate conformations of the structure. For example, a hexose molecule molecule can form the 5...
by Elizabeth Swanberg | Dec 16, 2018 | General Tools, Tools
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...
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...
