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Modeling with DNA/RNA

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...

Homology Modeling Tutorial

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...

Loop Rebuild

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...

Ligand Position Restraint

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...

How to Run DDG

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...

Valid Names

If you see this error:  ‘Please ensure that your collection name contains only valid characters as defined at support.cyrusbio.com‘ You have entered a non-accepted symbol into a name field. Below are the only symbols that are allowed in name fields:...