Difference between revisions of "Homology Based Structure Predictions Hemochromatosis"

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Revision as of 17:01, 3 June 2012

Hemochromatosis>>Task 4: Homology based structure predictions

Riddle of the task

After endless battles and deadly traps you have finally reached the tomb's final chamber. As you enter it you notice that there is no sign of the treasures that were promised by the old map you found months ago. Suddenly you hear a loud noise behind you and a solid wall of stone blocks the only entrance into the room. You are trapped! You look around and notice something on the walls. On the left wall are four runes in an ancient language. Luckily its the same language as the notes on the map you deciphered and they translate into four single letters:

  • C N O I

On the opposite wall you can see four simple symbols:

  • a triangle
  • a square
  • a circle
  • and a diamond (dt. Raute)

After further investigation you notice that the four symbols can be pushed into the wall, but you don't know what would happen and which one(s) to push.

What do you do?


Some hints:

  • You only have to push one button and only once.

Short Task Description

Detailed description: Homology based structure predictions

Protocol

A protocol with a description of the data acquisition and other scripts used for this task is available here.

PDB templates

In order to find templates for our models we performed several searches for homologs with COMA and HHPred. We also reused the sequences from Task 2. However none of these methods yielded homologs with a sequence identity above 40% (except 1a6z which is HFE itself) that could be mapped to a PDB structure. The best results for COMA and HHPred are listed in <xr id="coma_t"/> and <xr id="hhpred_t"/> respectively. Therefore we could not generate models with a sequence identity above 80% and the 40%-80% range was limited to its lower bound. In addition to those shown below, we also used 2iad_B (P01921, 21.10% identity) from task 2.

<figtable id="coma_t">

PDB ID e-Value Identities Positives
1a6z_A 1.00E-63 100% 100%
1t7v_A 1.20E-63 34% 62%
3nwm_A 1.60E-57 30% 57%
1frt_A 4.90E-65 28% 66%
2wy3_A 2.80E-63 26% 66%
3ov6_A 2.70E-55 20% 67%
1u58_A 1.00E-54 19% 59%
3d2u_A 7.50E-60 16% 70%
3dbx_A 9.70E-59 16% 71%
3it8_D 3.40E-52 15% 65%
TODO: COMA: Top10 (e-Value) sorted by Identities.

</figtable>

<figtable id="hhpred_t">

PDB ID e-Value Identities Similarity
1a6z_A 1.80E-69 100% 1.623
1k5n_A 2.80E-68 40% 0.725
1s7q_A 5.80E-78 37% 0.655
1t7v_A 7.40E-68 36% 0.702
3p73_A 1.10E-69 35% 0.638
3bev_A 1.00E-69 34% 0.684
2yf1_A 2.40E-74 32% 0.617
1zs8_A 7.30E-68 30% 0.553
2wy3_A 3.30E-68 29% 0.496
1cd1_A 1.60E-67 21% 0.394
TODO: HHpred: Top10 (e-Value) sorted by Identities.

</figtable>


Modeller


1k5nA


1zs8A


2iadB


3dbxA


MSA1


MSA2


MSA3


Evaluation

<figtable id="modeller_scores_native">

Model Common residues TM-Score GDT-TS GDT-HA TM-Align Weighted RMSD
1K5N_2d 272 0.1686 0.0846 0.0487 0.83298 2.200 (over 272 atoms)
1K5N_simple 272 0.1649 0.0846 0.0506 0.83358 2.325 (over 272 atoms)
1ZS8_2d 272 0.1698 0.0827 0.0432 0.85494 1.642 (over 272 atoms)
1ZS8_simple 272 0.1550 0.0790 0.0423 0.79841 2.302 (over 271 atoms)
2IAD_2d 272 0.1725 0.0836 0.0460 0.49103 2.166 (over 269 atoms)
2IAD_simple 272 0.1337 0.0607 0.0349 0.40162 3.705 (over 272 atoms)
3DBX_2d 272 0.1742 0.0892 0.0496 0.81698 2.374 (over 267 atoms)
3DBX_simple 272 0.1684 0.0882 0.0496 0.86512 1.524 (over 267 atoms)
MSA1 272 0.1680 0.0855 0.0496 0.83014 2.366 (over 270 atoms)
MSA2 272 0.3218 0.1811 0.0855 0.72682 1.889 (over 270 atoms)
MSA3 272 0.1530 0.0708 0.0358 0.40265 3.679 (over 272 atoms)
TODO: NATIVE.

</figtable>

<figtable id="modeller_scores_complex">

Model Common residues TM-Score GDT-TS GDT-HA TM-Align Weighted RMSD
1K5N_2d 272 0.1674 0.0800 0.0469 0.85238 1.986 (over 272 atoms)
1K5N_simple 272 0.1638 0.0800 0.0478 0.83836 2.142 (over 272 atoms)
1ZS8_2d 272 0.1715 0.0827 0.0450 0.86026 1.720 (over 272 atoms)
1ZS8_simple 272 0.1550 0.0790 0.0414 0.82124 2.059 (over 271 atoms)
2IAD_2d 272 0.1706 0.0836 0.0441 0.48549 2.279 (over 269 atoms)
2IAD_simple 272 0.1318 0.0653 0.0358 0.40088 3.655 (over 272 atoms)
3DBX_2d 272 0.1737 0.0873 0.0487 0.83662 2.088 (over 269 atoms)
3DBX_simple 272 0.1687 0.0901 0.0515 0.86877 1.492 (over 269 atoms)
MSA1 272 0.1698 0.0873 0.0524 0.84313 2.150 (over 270 atoms)
MSA2 272 0.3223 0.1783 0.0846 0.70465 2.011 (over 270 atoms)
MSA3 272 0.1574 0.0754 0.0377 0.40026 3.637 (over 272 atoms)
TODO: COMPLEX.

</figtable>


SwissModel


1k5nA

<figtable id="swiss_1k5nA_stats">

TODO
TODO
TODO
TODO
TODO

</figtable>


1zs8A

<figtable id="swiss_1zs8A_stats">

TODO
TODO
TODO
TODO
TODO

</figtable>


2iadB

<figtable id="swiss_2iadB_stats">

TODO
TODO
TODO
TODO

</figtable>


3dbxA

<figtable id="swiss_3dbxA_stats">

TODO
TODO
TODO
TODO

</figtable>


Evaluation

<figtable id="swiss_scores_native">

Model Common residues TM-Score GDT-TS GDT-HA TM-Align Weighted RMSD
1k5nA 250 0.1626 0.0809 0.0478 0.84456 2.121 (over 272 atoms)
1zs8A 249 0.1449 0.0662 0.0377 0.83755 1.514 (over 271 atoms)
2iadB 165 0.1218 0.0680 0.0450 0.50849 2.805 (over 187 atoms)
3dbxA 252 0.1684 0.0836 0.0478 0.89308 1.111 (over 272 atoms)
TODO: NATIVE.

</figtable>

<figtable id="swiss_scores_complex">

Model Common residues TM-Score GDT-TS GDT-HA TM-Align Weighted RMSD
1k5nA 250 0.1611 0.0781 0.0469 0.85087 2.009 (over 272 atoms)
1zs8A 249 0.1450 0.0689 0.0377 0.83904 1.501 (over 271 atoms)
2iadB 165 0.1201 0.0671 0.0432 0.49068 3.172 (over 187 atoms)
3dbxA 252 0.1679 0.0818 0.0460 0.88762 1.203 (over 272 atoms)
TODO: COMPLEX.

</figtable>


I-Tasser

Job still running (~10hrs)...


Evaluation


3D-Jigsaw


Evaluation

<figtable id="scores_native">

Model Common residues TM-Score GDT-TS GDT-HA TM-Align Weighted RMSD
model_1 272 0.1647 0.0864 0.0533 0.83038 2.359 (over 272 atoms)
model_2 272 0.1648 0.0873 0.0542 0.83125 2.351 (over 272 atoms)
model_3 272 0.1648 0.0873 0.0542 0.83127 2.350 (over 272 atoms)
model_4 272 0.1648 0.0873 0.0542 0.83127 2.350 (over 272 atoms)
model_5 272 0.1648 0.0873 0.0542 0.83127 2.350 (over 272 atoms)
TODO: NATIVE.

</figtable>

<figtable id="scores_complex">

Model Common residues TM-Score GDT-TS GDT-HA TM-Align Weighted RMSD
model_1 272 0.1637 0.0836 0.0506 0.83550 2.166 (over 272 atoms)
model_2 272 0.1637 0.0836 0.0506 0.83622 2.158 (over 272 atoms)
model_3 272 0.1637 0.0836 0.0506 0.83627 2.157 (over 272 atoms)
model_4 272 0.1637 0.0836 0.0506 0.83625 2.158 (over 272 atoms)
model_5 272 0.1637 0.0836 0.0506 0.83626 2.157 (over 272 atoms)
TODO: COMPLEX.

</figtable>


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