Loop Modeling

[Alex Brown <abrown@nimr.mrc.ac.uk>]

Dear Modellers,

I have been running through the examples in the Fiser and Sali paper 
concerning the modeling of the loop in cpCN-V (circularly permuted 
cyanovirin). I used the given scripts, modifying it to allow the 
modeling of different linker lengths, from 6 to 12 residues, as 
suggested in the paper. 200 final models of each linker were obtained, 
the model with the lowest energy score (objective function) being 
selected in each case. This gave the following table of results:
Length (aa)	Residues	Objective Function	Model #	File Name
   6                          49-54              21.6408                
119	cpCN-V.BL06
   7                          48-54              
12.1955                  49	cpCN-V.BL07
   7                          49-55              33.0729                
118	cpCN-V.BL07a
   8                          47-54              7.5401                  
153	cpCN-V.BL08
   8                          49-56              35.8842                
152	cpCN-V.BL08a
   8                          48-55              31.0163                
117	cpCN-V.BL08b
   9                          46-54              
12.1449                  95	cpCN-V.BL09
   9                          49-57              
24.4132                  39	cpCN-V.BL09a
   9                          47-55              29.1883                
145	cpCN-V.BL09b
   9                          48-56              27.4328                
115	cpCN-V.BL09c
 10                          46-55              28.5179                
184	cpCN-V.BL10
 10                          47-56              29.004                  
199	cpCN-V.BL10a
 10                          48-57              31.8589                  
25	cpCN-V.BL10b
 11                          46-56              18.1581                
109	cpCN-V.BL11
 11                          47-57              22.4939                
189	cpCN-V.BL11a
 12                          46-57              27.0164                
198	cpCN-V.BL12
My question is, can I take the 'best' loop model as being that with the 
lowest objective function (i.e. model cpCN-V.BL08, objective function 
7.5401).
I did wonder how my results compared with those obtained by Fiser and 
Sali, but I have been unable to find this.
Cheers,

Alex Brown

PS. I'm running Modeller v6.2 on Mac OS X (Darwin). Each modeling run 
(200 loop models) took 6-10 hours !!!!