by Elizabeth Swanberg | Jan 20, 2019 | Advanced use of Design, Workflows
Download "Using HM & CAD Together"...
by Elizabeth Swanberg | Jan 20, 2019 | Antibodies, Workflows
Click Here to Download This Article as a PDF INTRODUCTION The overarching goal of this workflow is to show Bench users how they may use their understanding of a complex protein-protein interface to generate specificity variants on that sequence, yielding orthogonal...
by Elizabeth Swanberg | Jan 20, 2019 | Analyzing Results, Workflows
How to analyze output structure quality from HM DETERMINING CONVERGENCE 1.) How close are the top models to one another? If the top models are tightly converged (especially in the helices and sheets), that is a good indication of a high quality model. The five models...
by Elizabeth Swanberg | Jan 8, 2019 | Analyzing Results, Workflows
INTRODUCTION TO PROTEIN DESIGN RESULTS Our Design tools are often used as a way to find multiple mutations that improve Rosetta Energy. We recommend running 100 repeats of a design. Then look at the range of results to find favorable mutations. Instructions on how to...
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...
