I'm trying to use ab initio modelling to predict the structure of a ~140 AA natively disordered domain of a protein which I plan to use later to stitch onto the rest of the protein. I produced 100,000 model structures following this tutorial (https://www.rosettacommons.org/docs/latest/application_documentation/structure_prediction/abinitio-relax) except without the -kill-hairpins option since it’s intrinsically disordered. I then used caliber to cluster the structures based on score as follows with the thresholds listed:
All – 14.01284
Top 10,000 – 13.79987
Top 5,000 – 13.75388
Top 1,000 – 13.65071
Top 500 – 13.63761
These almost always gave two top clusters with margin < 10%. I’m new to this and was worried that this might indicate that the modelling isn’t working since the thresholds are still high after this many models. Additionally, clustering with a threshold of 4.0 gives clusters of size 1.
Is this high of threshold expected or is there something that I should change to potentially give better models? Also, does the potential for multiple states, e.g. 2 state model, mess with clustering?
Thanks in advance!