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 !!!!