Difference between revisions of "Task 5 (MSUD)"
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Revision as of 14:00, 8 June 2013
Contents
Results
Modeller
Swissmodel
In the output of Swissmodel, almost all scores reported are 0 or not shown, probably due to an error in the program. The only score reported is the Anolea (atomic empirical mean force potential), which measures if the amino acids are in a favorable energy environment.
High sequence identity template
The following diagram shows the Anolea for the model build with 2BFE as template.
Almost all residues are in a favorable energy environment (negative Anolea values) and only some small parts of the protein structure are in an unfavorable one (positive values).
Low sequence identity template
Anolea for the model build with 3EXG as template:
Only a small percentage of the residues is in a favorable energy environment, but most parts of the protein are unfavorable.
iTasser
For the five alternative models that are predicted by iTasser, the C-scores are shown in the following table. The C-score is a confidence score that ranges from -5 to 2. A higher (less negative) score indicates a better quality of the model.
| template | model1 | model2 | model3 | model4 | model5 |
|---|---|---|---|---|---|
| 2BFE | -0.83 | -1.25 | -2.12 | -2.36 | -1.98 |
| 3EXG | -1.86 | -2.02 | -2.43 | -2.49 | -2.97 |
The models build with the high sequence identity template have a better average quality than those build with the low sequence identity template. But also the quality of models build with the same template deviate a lot from each other.
Evaluation of models
To compare the calculated models to the reference structure 1U5B, we report RMSD and GDT_TS. The score GDT_TS combines GDT (global distance test) values calculated with several distance cutoffs.
High sequence identity template
| Modeller | Swissmodel | iTasser, model1 | iTasser, model2 | iTasser, model3 | iTasser, model4 | iTasser, model5 | |
|---|---|---|---|---|---|---|---|
| GDT_TS | 96.0 | 89.1 | 95.5 | 88.5 | 94.9 | 96.9 | |
| RMSD | 1.7 | 2.9 | 1.0 | 3.1 | 1.5 | 0.8 |
Low sequence identity template
| Modeller | Swissmodel | iTasser, model1 | iTasser, model2 | iTasser, model3 | iTasser, model4 | iTasser, model5 | |
|---|---|---|---|---|---|---|---|
| GDT_TS | 61.7 | 68.4 | 66.0 | 66.6 | 69.0 | 69.1 | |
| RMSD | 9.7 | 14.5 | 13.9 | 14.0 | 15.4 | 15.4 |
