by Elizabeth Swanberg | Apr 22, 2019 | Introductory Workflows, Workflows
Delta Delta G (DDG) is a metric for predicting how a single point mutation will affect protein stability. To read more background information on DDG click here. 1.) Begin in CAD by clicking the folder on the left that contains your protein structure to bring it into...
by Elizabeth Swanberg | Jan 20, 2019 | Introductory Workflows, Workflows
INTERFACE DDG WORKFLOW The free energy of an interface single point mutation (change in binding free energy) can be calculated using this workflow. Here we will look at mutations on the alpha-helical peptide BHRF1 in complex with the Bim BH3 domain, 2WH6. STEP BY...
by Elizabeth Swanberg | Dec 31, 2018 | Introductory Workflows, Workflows
BACKGROUND A protein Position Specific Scoring Matrix (PSSM) takes the alignment of your protein to a list of homologs and counts the amino acids found at each position for the homologs. This is an easy way of measuring evolutionarily related mutations accepted at...
by Elizabeth Swanberg | Dec 20, 2018 | Introductory Workflows, Workflows
There are three design methods that you can run in CAD: Design, Flex Design, and Relax Design. They are all set up in the same way using the following steps… 1.) LOAD A STRUCTURE Click on , which will open a new tab in the center window. Load a structure into...
