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RosettaCM: threading okay, but hybridize loses many secondary structure

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RosettaCM: threading okay, but hybridize loses many secondary structure

I use two templates to run the RosettaCM, each template representing different parts of the target. The threading step can retain most of the secondary structure. However, when doing the hybridize step, one part in the target loses half of its beta-sheets. Is this a common issue?

Post Situation: 
Wed, 2021-06-23 13:51


The key thing to know here is that hybridize works best when it has templates that cover all domains.  When it starts with a template that only covers half the structure it starts out with the other half as basically an extended chain and then works to fold the protein from there


To get around this, try making a pdb file with both templates in a single pdb file (and with the two chains oriented approximately as you would expect them to be)

This is not a very scientifically sound way of doing things, but i have done it before to get starting points that  I hope to work with more experimental data later.


As an alternative I would suggest trying the robetta server -- it is quite good

Wed, 2021-06-23 22:14

Hi, this is a very good idea! Pre-treat the templates into one single PDB will minimise the incorrect guess. Thanks a lot!

Thu, 2021-06-24 10:16