On 12/27/14 7:35 PM, Adhikari, Badri (MU-Student) wrote: > I used Modeller to reconstruct around a 100 proteins with true > residue-residue contacts and secondary structure information. I could > reconstruct only a few proteins with high accuracy. Below is a sample > script I used for Modelling. I did not use any templates. (I found that > Modeller satisfies more contact restraints when I provided a template > with just one residue’s coordinates instead of an extended structure as > a template.) I wonder why Modeller could not satisfy true contact > restraints. Is there any specific way to reconstruct proteins using true > residue contacts?
You need a lot of these contacts to model a protein. Look at the restraint file from a typical Modeller run - it includes a large number of atom-atom distances with a wide span of residue ranges. I'm assuming you have more than 4 CA/CB contacts, but you probably don't have enough.
In addition, secondary structure restraints are pretty weak (they're more of a "suggestion") and are unlikely to force the protein to adopt that secondary structure unless it's pretty close to start with.
Ben Webb, Modeller Caretaker