by Elizabeth Swanberg | Sep 5, 2019 | FAQs
Cyrus Bench is meant to be provide an easy-to-use GUI so you can run Rosetta without the months of necessary training that are needed for the full version of Rosetta. Bench has the majority of Rosetta tools that are needed for most structure prediction, modeling or...
by Elizabeth Swanberg | Sep 3, 2019 | Using Pymol with Bench, Workflows
Click to Download Zip file for...
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 | Aug 29, 2019 | Background, Background on Homology Modeling
Click to Download HM Diagram Outlined below is a diagram and step-by-step descriptions of how Homology Modeling (HM) runs. HM is the easiest tool to run in CAD, but it performs a complex set of functions. You can run HM by inputting a sequence and come back later to...
by Elizabeth Swanberg | Aug 28, 2019 | FAQs
Cyrus Bench has implemented DNA/RNA handling in order to allow loading and modeling with these highly biologically-relevant molecules. Rosetta is excellent at modeling with nucleotides present. It has been successful at modeling proteins with DNA and RNA for deriving...
by Elizabeth Swanberg | Jun 5, 2019 | Getting Started, Tutorials
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...
by Elizabeth Swanberg | Jun 5, 2019 | Getting Started
Homology Modeling (HM) is the most effective method for predicting protein structure from its sequence. This tool uses the structures of homologous proteins, or protein fragments, as an estimate for your protein structure and then models conformational differences...
by Elizabeth Swanberg | May 21, 2019 | Actions, Tools
NOTE: An error message will appear if one or more CA…CA distances are detected to be too far apart in your structure after you click ‘Save and Run’. You will get this error if the distance in the starting coordinates for the loop you are attempting...
by Elizabeth Swanberg | May 16, 2019 | Actions, Tools
OVERVIEW Restrain Ligands is an option that can be activated during Repack, Minimize, Loop Rebuild, or Design. This is intended to freeze the molecule in place in relation to the protein during modeling. Warning: Only turn this on if you want the ligand to stay in...
