by Elizabeth Swanberg | Sep 18, 2019 | Structure Prediction
OVERVIEW 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...
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...
by Elizabeth Swanberg | Jan 2, 2019 | General Tools, Tools
WHAT IS THE SEQUENCE LOGO? The Sequence Logo is a tool that summarizes the residue(s) at each position across the sequence(s) that has been selected. It is especially useful when beginning to analyze sequences from design results. HOW TO ACCESS THE SEQUENCE LOGO To...
by Elizabeth Swanberg | Jan 2, 2019 | General Tools, Tools
1.) To enter scatter plot view, navigate to a collection with multiple structures and click at the bottom-right as shown below, and select 2.) Once in scatter plot view, you can choose which score terms to plot on the X and Y axes. 3.) You can select the points...
by Elizabeth Swanberg | Jan 2, 2019 | General Tools, Tools
You can now compare structures and sequences between any two (or more) collections directly in CAD. Previously this was not possible and required download of sequences and/or structures for viewing in other software. The Compare feature is available when a tab is open...
by Elizabeth Swanberg | Jan 2, 2019 | General Tools, Tools
Superpose is a feature that positions multiple structures on top of one another, based on a specified region of sequence that is shared among the different structures. The Superpose feature is useful for aligning and comparing multiple structures in the Structure...
by Elizabeth Swanberg | Jan 2, 2019 | General Tools
The Structure Viewer allows selected structures to be displayed where they will be presented in the bottom half of the center window as shown below. To display a structure protein click to the left of the structure name. If your protein does not appear, check that...
by Elizabeth Swanberg | Jan 2, 2019 | Structure Prediction, Tools
OVERVIEW HM Antibody is a structure prediction tool for the variable region of antibodies. The protocol assumes that your sequence is a naturally-occuring antibody, which means that there is a limit to how much your input can diverge from the norm. Often, users have...
by Elizabeth Swanberg | Dec 31, 2018 | Analysis, Tools
BACKGROUND Immunogenicity is the propensity of a molecule to provoke a response by the immune system. In many cases this is the desired behavior of the immune system, recognizing foreign objects and targeting them for neutralization or removal. However immunogenicity...
