by Elizabeth Swanberg | Jan 2, 2019 | Structure Prediction, Tools
OVERVIEW HM Antibody is a structure prediction tool for the variable region of antibodies. The protocol assumes that your sequence is a naturally-occuring antibody, which means that there is a limit to how much your input can diverge from the norm. Often, users have...
by Elizabeth Swanberg | Dec 31, 2018 | Analysis, Tools
BACKGROUND Immunogenicity is the propensity of a molecule to provoke a response by the immune system. In many cases this is the desired behavior of the immune system, recognizing foreign objects and targeting them for neutralization or removal. However immunogenicity...
by Elizabeth Swanberg | Dec 31, 2018 | Analysis, Tools
Delta Delta G (DDG) is a metric for predicting how a single point mutation will affect protein stability. DDG, often referred to as đ«đ«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...
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 21, 2018 | General Tools, Tools
OVERVIEW Loading a structure file into Bench is a two step process. Step One: Select which components of the structure file you wish to be included. Step Two: Bench processes the file contents to define all molecules in a way that allows Rosetta to understand the...
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 | General Tools, Tools
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 (â) +...
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 structureâs 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 | 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...
