Re: [modeller_usage] using Modeller for building models using contacts and secondary structures

[Modeller Caretaker <>]

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
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