Hi modeller users
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. My question is, What aspects must I take into consideration for loop refinement?, Is possible that the modeled structure do not need any loop refining?
Best regards Herbert
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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HERBERT MAX VENTHUR PE¥A -
Modeller Caretaker