Difference between revisions of "Homology modelling Gaucher Disease"
From Bioinformatikpedia
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| colspan=4 style="border-style: solid; border-width: 1px 0 1px 0; font-style: italic; text-align: center;" | < 30% sequence identity |
| colspan=4 style="border-style: solid; border-width: 1px 0 1px 0; font-style: italic; text-align: center;" | < 30% sequence identity |
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| 2 || 2wnw_A || 28.0 || 100.0 |
| 2 || 2wnw_A || 28.0 || 100.0 |
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| 3 || 3clw_A || 14.0 || 100.0 |
| 3 || 3clw_A || 14.0 || 100.0 |
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| − | |- style="color: |
+ | |- style="color:green; font-weight:bold" |
| 4 || 2y24_A || 18.0 || 100.0 |
| 4 || 2y24_A || 18.0 || 100.0 |
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| 7 || 3ik2_A || 14.0 || 99.2 |
| 7 || 3ik2_A || 14.0 || 99.2 |
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| − | |- style="color: |
+ | |- style="color:goldenrod; font-weight:bold" |
| 22 || 3nco_A || 11.0 || 97.7 |
| 22 || 3nco_A || 11.0 || 97.7 |
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| + | |- |
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| 28 || 1egz_A || 12.0 || 97.4 |
| 28 || 1egz_A || 12.0 || 97.4 |
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Revision as of 13:21, 29 May 2012
Contents
Template selection
<figtable id="tab:ss_mapping">
| Hit Nr | Template | Identity | HHsearch prob |
|---|---|---|---|
| > 80% sequence identity | |||
| 1 | 2nt0_A | 100.0 | 100.0 |
| 40% - 80% sequence identity | |||
| < 30% sequence identity | |||
| 2 | 2wnw_A | 28.0 | 100.0 |
| 3 | 3clw_A | 14.0 | 100.0 |
| 4 | 2y24_A | 18.0 | 100.0 |
| 5 | 3kl0_A | 19.0 | 100.0 |
| 6 | 3zr5_A | 17.0 | 100.0 |
| 7 | 3ik2_A | 14.0 | 99.2 |
| 22 | 3nco_A | 11.0 | 97.7 |
| 28 | 1egz_A | 12.0 | 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>
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 | 1.006 | 0.824 | 0.661 | 0.479 |
| 2y24_A | -42674 | 0.565 | 0.430 | 1.222 | 0.550 | 0.294 | 0.223 |
| 3nco_A | -27101 | 1.122 | 0.270 | 2.158 | 0.252 | 0.093 | 0.043 |
</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 | 1.006 | 0.824 | 0.661 | 0.479 |
| 2y24_A | -40131 | 1.001 | 0.360 | 1.222 | 0.550 | 0.294 | 0.223 |
| 3nco_A | -30244 | 0.689 | 0.240 | 2.158 | 0.252 | 0.093 | 0.043 |
</figtable>
