Task 5 (MSUD)

Results

Lab journal

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.

C-scores of structure models calculated with iTasser

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

Comparison of structure models (build with template 2BFE) to the reference structure 1U5B

	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

Comparison of structure models (build with template 3EXG) to the reference structure 1U5B

	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