Difference between revisions of "Homology modelling TSD"
(→SWISS-MODEL) |
(→Low sequence identity) |
||
| Line 78: | Line 78: | ||
The same occured for '''3nsm''' which has a sequence identity about 7% higher than 3gh5. A sequence identity lower than 30% seems to be too low for modelling. |
The same occured for '''3nsm''' which has a sequence identity about 7% higher than 3gh5. A sequence identity lower than 30% seems to be too low for modelling. |
||
<br style="clear:both;"> |
<br style="clear:both;"> |
||
| + | |||
| + | ===Evaluation=== |
||
| + | <figtable id="tab:swisseval"> |
||
| + | {| class="wikitable", style="width:550px; border-collapse: collapse; border-style: solid; border-width:0px; border-color: #000" |
||
| + | |-align="left" |
||
| + | ! style="border-style: solid; border-width: 0 0 2px 0" | |
||
| + | ! style="border-style: solid; border-width: 0 0 2px 0" | Residues in Common |
||
| + | ! style="border-style: solid; border-width: 0 0 2px 0" | TM |
||
| + | ! style="border-style: solid; border-width: 0 0 2px 0" | GDT-TS |
||
| + | ! style="border-style: solid; border-width: 0 0 2px 0" | GDT-HA |
||
| + | ! style="border-style: solid; border-width: 0 0 2px 0" | C-alpha RMSD |
||
| + | |- |
||
| + | ! style="border-style: solid; border-width: 0 0 0 0" align="left" rowspan="1" | 2gk1 |
||
| + | | style="border-style: solid; border-width: 0 0 0 0" | |
||
| + | | style="border-style: solid; border-width: 0 0 0 0" | |
||
| + | | style="border-style: solid; border-width: 0 0 0 0" | |
||
| + | | style="border-style: solid; border-width: 0 0 0 0" | |
||
| + | | style="border-style: solid; border-width: 0 0 0 0" | |
||
| + | |- |
||
| + | ! style="border-style: solid; border-width: 0 0 0 0" align="left" rowspan="1" | 1o7a |
||
| + | | style="border-style: solid; border-width: 0 0 0 0" | |
||
| + | | style="border-style: solid; border-width: 0 0 0 0" | |
||
| + | | style="border-style: solid; border-width: 0 0 0 0" | |
||
| + | | style="border-style: solid; border-width: 0 0 0 0" | |
||
| + | | style="border-style: solid; border-width: 0 0 0 0" | |
||
| + | |- |
||
| + | |} |
||
| + | '''Table TODO''': |
||
| + | </figtable> |
||
== iTasser == |
== iTasser == |
||
Revision as of 15:25, 31 May 2012
There will be no curiosity, no enjoyment of the process of life. All competing pleasures will be destroyed. But always — do not forget this, Winston — always there will be the intoxication of power, constantly increasing and constantly growing subtler. Always, at every moment, there will be the thrill of victory, the sensation of trampling on an enemy who is helpless. If you want a picture of the future, imagine a boot stamping on a human face — forever.
1984
Contents
Templates
Since similar sets were already collected for Task 2, the information was reused. In addition searches with HHpred on pdb70 and with COMA on pdb40 were performed. If two structures were mapped to the same Uniprot entry, only one, the 'most native' one, was used.
None of the searches revealed any structure with >80% sequence identity, other than the two already known structures 2gjx and 2gk1 which share 100% sequence identity. To still perform the task, 2gjx, which is the native structure <ref name="2gjxref">Lemieux,M. et al. (2006) Crystallographic Structure of Human beta-Hexosaminidase A: Interpretation of Tay-Sachs Mutations and Loss of GM2 Ganglioside Hydrolysis. Journal of molecular biology, 359, 913-29.</ref>, was chosen as reference and 2gk1, which has the inhibitor NGT bound, will be used as template.
<figtable id="tab:signals">
| PDB id | Sequence identity | Method | |
|---|---|---|---|
| > 80% identity | 2gk1 | 100% | Task2/HHpred/COMA |
| 40% - 80% identity | 1o7a_D | 56.6% | Task 2 |
| 3lmy_A | 54% | COMA | |
| < 30% identity | 3nsm_A | 27.5% | Task 2 |
| 3gh5_A | 20.7% | Task 2 |
Table TODO: </figtable>
Alignments
SWISS-MODEL
Default Modelling
Chosen template 2gjx_E.
High sequence identity
Medium Sequence identity
Low sequence identity
With the 3gh5 as template the automated SWISS-MODEL was not able to calculate a model structure for the Hex A subunit. Two alignments were produced, one with Blast and one with HHsearch. While the Blast alignment quality between target and template was too low to start with, the HHsearch alignment reached the next level and was sent to modelling but the building of a model was not successful.
The same occured for 3nsm which has a sequence identity about 7% higher than 3gh5. A sequence identity lower than 30% seems to be too low for modelling.
Evaluation
<figtable id="tab:swisseval">
| Residues in Common | TM | GDT-TS | GDT-HA | C-alpha RMSD | |
|---|---|---|---|---|---|
| 2gk1 | |||||
| 1o7a |
Table TODO: </figtable>
iTasser
Modeller
3D-Jigsaw
References
<references/>
