by Elizabeth Swanberg | Sep 3, 2019 | Using Pymol with Bench, Workflows
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by Elizabeth Swanberg | Aug 29, 2019 | Advanced use of Design, Workflows
One of the most effective ways to improve protein stability and solubility is to use evolutionary information to guide mutation selection. This workflow shows how you can create a multi-sequence alignment from homologs in the NCBI database, then sample the mutations...
by Elizabeth Swanberg | Aug 29, 2019 | Advanced use of Design, Workflows
Researchers often have a new sequence they want to model or use as a starting point for future design work. We have a quick and simple method for doing this 1.) Load the protein into CAD Use the as usual. Include or exclude any additional molecules in the file that...
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 | Advanced use of Design, Workflows
After running DDG, users often want to select mutations that are found to be favorable as a mutation set for Design. We are working on adding an automatic implementation for this in CAD, but in the meantime you can download a program that will do it for you. This tool...
by Elizabeth Swanberg | Jan 20, 2019 | Advanced use of Design, Workflows
Workflows for rescoring protein-protein complex from other software, and disulfide bond removal with maintained overall...
by Elizabeth Swanberg | Jan 20, 2019 | Antibodies, Workflows
BACKGROUND B Cells can have surface antibodies that can bind proteins. This can elicit an immune response if other factors are present to activate the B Cell. One way to inhibit or increase antibody binding to a protein is to alter its surface residues to change the...
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...
