Homology Modeling Update

We have updated the Homology Modeling user interface, and have added the option to load multiple sequences at once. For more information on how to load a batch of sequences into HM, click here.

New Design Tool: FLEX DESIGN

Our newest CAD design tool is called Flex Design. This is similar to our current Design tool, but allows more backbone changes to occur in the area of design. This will allow more mutations to be sampled because the backbone can adjust to changes that are larger, smaller, or have a different polar nature. The backbone will only be allowed to make minor adjustments (within 0.5 Å ) in the region of design and the region up to 8 Å away.

Cyrus’s FlexDesign Action runs Rosetta’s CoupledMoves protocol, which has emerged as the best generalized tool for predicting affinity-improving mutations at either a protein/protein or a protein/small-molecule interface, when starting from an existing interface in need of improvement.

For a full description of Flex Design and how it relates to our original Design tool and a tool called Relax Design that will be released soon click here.

For a tutorial on how to run Flex Design click here.

Quick Mutating CAD Cyrus Biotechnology

Quick Mutating

New Controls for Structure Viewer

The ability to select structures to view in the center window has become easier to manipulate. When you select a collection in the left window, the structures in that collection will become listed in the center window. Previously, you were only able to select structures to see in the viewer by individually clicking the eye icon to the left of the structure.

CAD Cyrus Biotechnology

We have introduced multi-select to the collections panel, so many checkboxes can be checked with the same ***click + shift-click*** shortcut that can be used in the structure viewer. Now, you will also be able to send structures to the viewer by clicking a new eye icon found above that list of structures in the center window.

CAD Cyrus Biotechnology

You can check one or more structure boxes, click the new eye icon, then select “Add to Structure Viewer” from the drop down menu to bring selected structures into the viewer. You can also select structures to be removed from the structure viewer or replace structures with a different set.

CAD Cyrus Biotechnology

One final change is that clicking a structure row will now select or deselect the structure box rather than effect whether its eye icon is active.

Import Collection

You can import a collection of structures from another project. First, go to the Structure Loader tab of the project where you need the collection to end up. In the center region you will see a pull down arrow so that you can select a project. Then select from the collection pull down window. Clicking Import will pull that collection into your project.

CAD Cyrus Biotechnology

Import Collection

Sequence Logo

Sequence Logo is a tool that can be used after running CAD Design or Flex Design. The Design methods in Bench allow for sequence mutation in the search for improved stability or affinity. The Logo plot makes it simple to visualize the sequence variation at each mutatable position once the calculation is complete. Residue mutations accepted at each position and the frequency with which they are observed are reflected in the Logo plot …more

Sequence tool CAD Cyrus Biotechnology

Sequence Logo

Loop rebuild

We’ve added the Loop Rebuild action to CAD. This tool is suitable for resampling the conformations of existing loops. ‘Aggressive mode’ will delete the starting loop conformation, proceeding from scratch. …more

Loop rebuild CAD Cyrus Biotechnology

Loop Rebuild

Select sequence differences between visible structures

Clicking the ‘eye’ icon next to more than one structure will enable the ‘Differences Selector’ button. When this button is clicked, each position at which residues differ will be highlighted. Clicking ‘Create’ will create a selector containing these positions.

Differences Selector CAD Cyrus Biotechnology

Differences Selector

Filter by residue type

Clicking the ‘eye’ icon next to more than one structure, and selecting a desired region, will enable the ‘Filter’ button. We have added filters to filter by residue types, clicking on an option will filter your current selection, unselecting all residues which don’t pass the filter. Clicking ‘Create’ will create a re-usable selector for this selection.

Residue Filters CAD Cyrus Biotechnology

Residue FIlters

Streamlined FASTA downloads

We’ve added a backend route for FASTA downloading, meaning thousands of FASTAs can now be downloaded quickly and reliably.

FASTA download CAD Cyrus Biotechnology

FASTA download

Improvements to structure loader

In the top left panel you will see ‘New structure’ has been replaced with ‘Structure Loader’. Clicking this button will take you to a structure loader tab, where you can now upload files while continuing to work on your project in other tabs. Simply enter all RCSB codes for structures you’d like uploaded, separated with commas, and click the button to the right or press ‘Enter’. If you’d like to upload PDB files instead, click the button to the right, and click + shift-click to select all desired PDBs.

Structure Loader CAD Cyrus Biotechnology

Structure Loader