Difference between revisions of "Task 5 (MSUD)"

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(Evaluation of models)
(Evaluation of models)
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|+ Comparison of structure models build with template 2BFE
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|+ Comparison of structure models (build with template 2BFE) to the reference structure 1U5B
 
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! !! Modeller !! Swissmodel !! iTasser, model1 !! iTasser, model2 !! iTasser, model3 !! iTasser, model4 !! iTasser, model5
 
! !! Modeller !! Swissmodel !! iTasser, model1 !! iTasser, model2 !! iTasser, model3 !! iTasser, model4 !! iTasser, model5
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{| class="wikitable" border="1" style="text-align:center;width:800px"
 
{| class="wikitable" border="1" style="text-align:center;width:800px"
|+ Comparison of structure models build with template 3EXG
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|+ Comparison of structure models (build with template 3EXG) to the reference structure 1U5B
 
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! !! Modeller !! Swissmodel !! iTasser, model1 !! iTasser, model2 !! iTasser, model3 !! iTasser, model4 !! iTasser, model5
 
! !! Modeller !! Swissmodel !! iTasser, model1 !! iTasser, model2 !! iTasser, model3 !! iTasser, model4 !! iTasser, model5

Revision as of 16:53, 7 June 2013

Results

Lab journal

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.

MSUD swissmodel 2bfe anolea.jpg

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:

MSUD swissmodel 3exg anolea.jpg

Only a small percentage of the residues is in a favorable energy environment, but most parts of the protein are unfavorable.

iTasser

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


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

Discussion