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....
