Homology Based Structure Predictions Hemochromatosis

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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


1zs8A


2iadB


3dbxA


Evaluation

<figtable id="swiss_scores_native">

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

</figtable>

<figtable id="swiss_scores_complex">

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

</figtable>


I-Tasser

Job still running (~10hrs)...


Evaluation


3D-Jigsaw


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