Difference between revisions of "Homology modelling Gaucher Disease"
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=== Using local HHsearch alignments === |
=== Using local HHsearch alignments === |
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| − | |[[File:modeller-hhsearch-local-1ogs_A-2wnw_A-ali.png|thumb|150px|2wnw_A]] |
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| − | |[[File:modeller-hhsearch-local-1ogs_A-2y24_A-ali.png|thumb|150px|2y24_A]] |
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| − | |[[File:modeller-hhsearch-local-1ogs_A-3nco_A-ali.png|thumb|150px|3nco_A]] |
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|[[File:modeller-hhsearch-local-1ogs_A-2wnw_A.png|thumb|150px|2wnw_A]] |
|[[File:modeller-hhsearch-local-1ogs_A-2wnw_A.png|thumb|150px|2wnw_A]] |
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Revision as of 16:46, 29 May 2012
Contents
Template selection
<figtable id="tab:ss_mapping">
| Hit Nr | Template | Identity | Query HMM | Prob |
|---|---|---|---|---|
| > 80% sequence identity | ||||
| 1 | 2nt0_A | 100.0 | 1-497 | 100.0 |
| 40% - 80% sequence identity | ||||
| < 30% sequence identity | ||||
| 2 | 2wnw_A | 28.0 | 36-496 | 100.0 |
| 3 | 3clw_A | 14.0 | 64-495 | 100.0 |
| 4 | 2y24_A | 18.0 | 66-495 | 100.0 |
| 5 | 3kl0_A | 19.0 | 65-495 | 100.0 |
| 6 | 3zr5_A | 17.0 | 65-494 | 100.0 |
| 7 | 3ik2_A | 14.0 | 65-495 | 99.2 |
| 22 | 3nco_A | 11.0 | 113-384 | 97.7 |
| 28 | 1egz_A | 12.0 | 113-387 | 97.4 |
</figtable>
Modeller
Single-template modeling
<figtable id="tab:modeller_results">
| Template | DOPE | DOPE z-score | QMEAN6 | RMSD | TM-score | GDT_TS | GTD_HA |
|---|---|---|---|---|---|---|---|
| 2wnw_A | -55925 | -0.471 | 0.689 | 1.006 | 0.824 | 0.661 | 0.479 |
| 2y24_A | -47194 | 0.777 | 0.376 | 1.222 | 0.550 | 0.294 | 0.223 |
| 3nco_A | -44033 | 1.224 | 0.139 | 2.158 | 0.252 | 0.093 | 0.043 |
</figtable>
Multiple-template modeling
<figtable id="tab:modeller_results">
| Template | DOPE | DOPE z-score | QMEAN6 | RMSD | TM-score | GDT_TS | GTD_HA |
|---|---|---|---|---|---|---|---|
| 2wnw_A-2y24_A-3kl0 | -39084 | 1.930 | 0.314 | 1.987 | 0.465 | 0.277 | 0.179 |
| 2wnw_A-3nco_A | -46962 | 0.807 | 0.556 | 1.256 | 0.778 | 0.593 | 0.409 |
| 3ik2_A-3nco_A-1egz_A | -25391 | 0.3881 | 0.101 | 6.607 | 0.241 | 0.062 | 0.029 |
</figtable>
Using global HHsearch alignments
<figtable id="tab:modeller-hhsearch-results">
| Template | DOPE | DOPE z-score | QMEAN6 | RMSD | TM-score | GDT_TS | GTD_HA |
|---|---|---|---|---|---|---|---|
| 2wnw_A | -54695 | -0.295 | 0.726 | 1.079 | 0.869 | 0.732 | 0.538 |
| 2y24_A | -47256 | 0.765 | 0.566 | 1.640 | 0.722 | 0.553 | 0.386 |
| 3nco_A | -32577 | 2.857 | 0.272 | 9.757 | 0.398 | 0.235 | 0.131 |
</figtable>
Using local HHsearch alignments
<figtable id="tab:modeller-hhsearch-local-results">
| Template | DOPE | DOPE z-score | QMEAN6 | RMSD | TM-score | GDT_TS | GTD_HA |
|---|---|---|---|---|---|---|---|
| 2wnw_A | -53593 | -0.744 | 0.689 | 1.003 | 0.866 | 0.731 | 0.532 |
| 2y24_A | -46290 | -0.030 | 0.376 | 1.162 | 0.724 | 0.563 | 0.381 |
| 3nco_A | -25047 | 0.886 | 0.139 | 1.827 | 0.402 | 0.245 | 0.138 |
</figtable>
SWISS-MODEL
Automated mode
<figtable id="tab:modeller_results">
| Template | DOPE | DOPE z-score | QMEAN6 | RMSD | TM-score | GDT_TS | GTD_HA |
|---|---|---|---|---|---|---|---|
| 2wnw_A | -53863 | -0.786 | 0.530 | 1.003 | 0.858 | 0.723 | 0.540 |
| 2y24_A | -42674 | 0.565 | 0.430 | 1.100 | 0.712 | 0.539 | 0.382 |
| 3nco_A | -27101 | 2.109 | 0.270 | 2.158 | 0.422 | 0.252 | 0.138 |
</figtable>
Alignment mode
<figtable id="tab:modeller_results">
| Template | DOPE | DOPE z-score | QMEAN6 | RMSD | TM-score | GDT_TS | GTD_HA |
|---|---|---|---|---|---|---|---|
| 2wnw_A | -53963 | -0.788 | 0.540 | 1.011 | 0.859 | 0.722 | 0.536 |
| 2y24_A | -40131 | 1.055 | 0.360 | 1.222 | 0.510 | 0.238 | 0.067 |
| 3nco_A | -30244 | 0.689 | 0.240 | 2.001 | 0.426 | 0.247 | 0.135 |
</figtable>
