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Re: [modeller_usage] Loop refining

On 09/15/2013 04:11 PM, HERBERT MAX VENTHUR PE¥A wrote:

I've already modeled a structure of an OBP (insect proteins). I picked
the structure  (pdb) with the lowest DOPE score, which is actually has
the best stereochemical quality according to Procheck. After that, I
used the script for "loop refining" in a positive range of values
according to Anolea (showed as red bars). I was waiting a better
stereochemical quality after the loop refinement, however, more bad
contacts among residues and low allowed positions were obtained.
Loop modeling aims to sample native-like loops in the region you select. But you'll need to produce a large number of models (maybe 300 or more) to hope to get close to native. I would expect to see a lot of suboptimal models in there too - which you'd need to throw out. 


	Ben Webb, Modeller Caretaker
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