by Elizabeth Swanberg | Jan 8, 2019 | FAQs
In Homology Modeling, each alignment is given a likelihood score. This score attempts to calculate the probability that a particular template/alignment is among the top 2% GDT (Global Distance Test, Zemla et al., Proteins, 1999) score for a particular target. The...
by Elizabeth Swanberg | Jan 8, 2019 | FAQs
This is a very common question. In general there are two ways in Bench to tell whether a sequence is good: 1) By checking the structure’s score and other metrics in the output of a design: overall lower scores are better and 2) By computational testing with...
by Elizabeth Swanberg | Jan 8, 2019 | FAQs
For most CAD modeling tools, a single run will be insufficient at sampling the variety of protein conformations. Each run begins with its own unique trajectory and one run will have a slightly different answer from another run. The more possible conformations your...
by Elizabeth Swanberg | Jan 8, 2019 | FAQs
Prepare has been tuned to optimally minimize the energy of a structure so that it is ready for Design. It should not require any subsequent Repack/Minimize/Relax before going into Design. After Prepare, you can go ahead and run Design with the following number of...
by Elizabeth Swanberg | Jan 8, 2019 | FAQs
Although Cyrus offers best-in-class protein design, there are limits to what it is recommended to attempt. As seen in this question it is possible to redesign 20% or more of a sequence, but it requires many cycles with separate tools, not a single run through Design....
by Elizabeth Swanberg | Jan 8, 2019 | FAQs
You can export the sequences generated in Design by downloading the structures’ PDBs or FASTAs. Begin by opening the file containing your Design results. As shown below you will be able to select the structures you would like to download data for by checking the...
by Elizabeth Swanberg | Jan 8, 2019 | FAQs
The number of repeats and the unique combination of Actions you should run when making mutations to your protein will depend on two factors. First, how large will your following experimental tests be; how many sequences are you looking to generate? Second, what level...
by Elizabeth Swanberg | Jan 8, 2019 | FAQs
Cyrus Bench Loop Rebuild is currently in Beta testing. However, the method proposed is great and routinely used to do loop extensions. Here is a suggested workflow. 1.) Insert desired loop sequences into your FASTA sequence, then run in Homology Modeling as a...
by Elizabeth Swanberg | Jan 8, 2019 | FAQs
When looking for stabilizing mutations it is helpful to compare DDG results across different models. The standard deviation is normally 1-2 between models, so a DDG of less than -1 would be interesting to look at. For more information on how to run DDG and interpret...
by Elizabeth Swanberg | Jan 8, 2019 | FAQs
Yes, we plan on there eventually being a command-line interface for CAD. It will not expose the user to direct interaction with Rosetta, but will expand the power of existing CAD...
