Introduction to Cyrus Support Guides

Cyrus Bench includes many powerful tools for designing proteins, predicting structures, and reducing immunogenicity. We’ve created this Introduction to showcase the most important features in Bench and how to use them.

You can view all the articles in each category by clicking on the category names in the left side bar (Tools, Background, Workflows, Videos, FAQs).

To help you become familiar with these tools and features you may find it helpful to begin by following our tutorial series, and then explore additional workflows for specific projects.

Tutorial Series for Beginners:

These four tutorials will introduce you to many of the Structure Viewer features in CAD as well as how to run common actions such as Relax and Design. The tutorials and the content introduced in each is outlined below:

• Tutorial 1:
  • Structure Loader, Prepare, Structure Viewer, Compare, Superpose
• Tutorial 2:
  • Relax, Scatter Plot, Minimize
• Tutorial 3:
  • Design, Selector, Loop Rebuild
• Tutorial 4:
  • Relax, Minimize, Design, Sequence Logo, Compare

Homology Modeling Tutorials:

Another powerful tool available in Cyrus Bench is Homology Modeling (HM). For an introduction on how to run HM, from deciding whether your sequence will be a good fit to understanding your results, please follow the tutorial below:

• Homology Modeling Tutorial

There are additional in-depth tutorials describing how HM results can be used and analyzed:

• How to Analyze HM Output: Structure Quality Guide
• Using HM and CAD Together for Backbone Structure Redesign
• How to Align Two Domains Created Separately with HM
• Modeling a Homodimer Using a Monomer Created with HM

Specific Project Tutorials:

As you become more familiar with Cyrus Bench you may be interested in using tutorials tailored to more specific projects. Several common workflows are listed below:

• Introductory Workflows:
  • How to Set up a Design in CAD
  • Loading and Modeling with Small Molecules Present
  • How to Run DDG

• Advanced Use of Design:
  • Create Point Mutations Quickly
  • Using DDG for Protein-Protein Interface
  • Using HM with Design for Backbone Structure Re-design

• Antibodies:
  • Design a Protein to Affect Affinity to B-cell Antibodies
  • Designing Bispecific Antibodies

Explore the additional workflows available on the site by clicking here, delving into the the Workflows tab to the left, or using the Search bar at the top of the page.

For Expert Users:

Once you become familiar with the tools in CAD you may find it helpful to download the PDF below that lists out the steps for using tools in Cyrus Bench.