by Elizabeth Swanberg | Jan 20, 2019 | Advanced use of Design, Workflows
Download "Using HM & CAD Together"...
by Elizabeth Swanberg | Jan 20, 2019 | Tutorial Videos, Videos
This is a basic method for any oligomer. More complex protocols with more automation may also be introduced, but this is a generally applicable method that allows you flexibility, assuming that when you look at step (I.1) the homologs do not extensively interpenetrate...
by Elizabeth Swanberg | Jan 20, 2019 | Antibodies, Workflows
Click Here to Download This Article as a PDF INTRODUCTION The overarching goal of this workflow is to show Bench users how they may use their understanding of a complex protein-protein interface to generate specificity variants on that sequence, yielding orthogonal...
by Elizabeth Swanberg | Jan 20, 2019 | Analyzing Results, Workflows
How to analyze output structure quality from HM DETERMINING CONVERGENCE 1.) How close are the top models to one another? If the top models are tightly converged (especially in the helices and sheets), that is a good indication of a high quality model. The five models...
by Elizabeth Swanberg | Jan 15, 2019 | FAQs
If you are experiencing unusual behavior is CAD, we will be happy to help you fix the issue. Some issues can be resolved by closing all tabs, exiting CAD, and then reopening CAD. Some issues will disappear during this process because they are browser-related (we...
by Elizabeth Swanberg | Jan 15, 2019 | FAQs
When a structure is imported through the Structure Loader, Bench concatenates all chains in the PDB file into a single long string of residues. The chains will be in the same order as they appear in the PDB file. This reflects the protocol used by Rosetta. As a result...
by Elizabeth Swanberg | Jan 15, 2019 | FAQs
The RMSD values provided by Bench are calculated using the alpha carbon positions of the structures being...
by Elizabeth Swanberg | Jan 15, 2019 | FAQs
The scoring metrics from HM and CAD are listed below as they appear left to right (lower is better): Score is a summary of the Rosetta energy function, reported in Rosetta Energy Units. When no other specific considerations apply, this is how one should rank models....
by Elizabeth Swanberg | Jan 15, 2019 | FAQs
The Structure Viewer used in CAD and HM does not have a way to visualize disulfide bonds, but they will still be accounted for by Rosetta during any calculations. We are planning on switching viewers in the future to one that will allow for disulfide bond...
