I have performed a docking between a protein and a 15 residue peptide using flex pep dock. I have got a total score of around -1347, is this considered as good docking ? I am unable to predict whether the docking can be considered or not. Please help me. Thanks in advance:
The total score and other factors are as follows:
|
total_score |
I_sc |
fa_atr |
fa_dun |
fa_pair |
fa_rep |
fa_sol |
hbond_sc |
pep_sc |
pep_sc_noref |
rama |
rmsALL_if |
rmsBB |
rmsBB_if |
startRMSbb |
description |
|
-1347.095 |
-14.720 |
-5007.113 |
1134.600 |
-85.068 |
776.773 |
2460.776 |
-39.201 |
-8.295 |
-19.405 |
141.836 |
2.842 |
2.680 |
2.430 |
0.000 |
top_1.pdb |
|
-1343.080 |
-11.662 |
-4997.305 |
1134.889 |
-84.667 |
773.714 |
2457.896 |
-39.826 |
-5.309 |
-16.419 |
142.413 |
2.411 |
1.188 |
1.205 |
0.000 |
top_2.pdb |
|
-1342.016 |
-17.091 |
-5003.941 |
1132.832 |
-84.844 |
782.667 |
2459.289 |
-39.885 |
-10.117 |
-21.227 |
142.670 |
2.212 |
1.501 |
1.516 |
0.000 |
top_3.pdb |
|
-1341.815 |
-14.740 |
-5012.769 |
1136.692 |
-83.429 |
778.716 |
2465.664 |
-39.519 |
-8.820 |
-19.930 |
142.253 |
2.434 |
2.203 |
2.015 |
0.000 |
top_4.pdb |
|
-1341.156 |
-17.032 |
-5004.029 |
1137.124 |
-84.009 |
776.288 |
2461.377 |
-39.548 |
-8.928 |
-20.038 |
142.564 |
2.178 |
1.044 |
1.057 |
0.000 |
top_5.pdb |
|
-1340.566 |
-15.159 |
-5013.151 |
1136.656 |
-83.377 |
779.321 |
2466.008 |
-40.593 |
-6.833 |
-17.943 |
142.152 |
2.704 |
2.653 |
2.466 |
0.000 |
top_6.pdb |
|
-1340.552 |
-13.753 |
-5011.181 |
1139.277 |
-84.528 |
776.843 |
2467.074 |
-39.732 |
-8.951 |
-20.061 |
141.948 |
1.898 |
1.583 |
1.467 |
0.000 |
top_7.pdb |
|
-1340.207 |
-14.188 |
-5003.347 |
1136.732 |
-84.222 |
781.371 |
2456.592 |
-39.093 |
-7.809 |
-18.919 |
141.985 |
6.767 |
5.835 |
6.127 |
0.000 |
top_8.pdb |
|
-1339.185 |
-14.238 |
-5018.549 |
1144.341 |
-85.171 |
780.477 |
2469.711 |
-39.545 |
-7.569 |
-18.679 |
141.185 |
1.937 |
1.613 |
1.484 |
0.000 |
top_9.pdb |
|
-1339.054 |
-15.704 |
-5007.212 |
1138.056 |
-83.308 |
778.395 |
2462.201 |
-39.708 |
-8.215 |
-19.325 |
142.234 |
2.347 |
0.831 |
0.865 |
0.000 |
top_10.pdb |
Hello,
In docking experiments it is common to sort your models for an acceptably good total_score in order to remove models with clashes and other poor properties and then sort these good models based on the interface score. In your case, model 3 and 5 are the best to look at based on secondary sorting by I_sc (interface score). A good rule of thumb is to select the top 10% by total_score then sort these by I_sc and look at these top scoring models.
Take a look at these docs as well if you haven't already. The advice I give is in the last paragraph of the Analyzing Results doc, written a little differently, of course.
https://www.rosettacommons.org/docs/latest/getting_started/Analyzing-Results
https://www.rosettacommons.org/docs/latest/getting_started/Rosetta-on-different-scales