Difference between revisions of "Homology modelling Gaucher Disease"

From Bioinformatikpedia
(→‎Modeller)
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| 0.062
  
| 0.062
 
| 0.029
  
| 0.029
  +
|}
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</figtable>
  +
  +
=== Using HHsearch alignments ===
  +
{|
  +
|[[File:modeller-hhsearch-1ogs_A-2wnw_A-ali.png|thumb|150px|2wnw_A]]
  +
|[[File:modeller-hhsearch-1ogs_A-2y24_A-ali.png|thumb|150px|2y24_A]]
  +
|[[File:modeller-hhsearch-1ogs_A-3nco_A-ali.png|thumb|150px|3nco_A]]
  +
|}
  +
  +
{|
  +
|[[File:modeller-hhsearch-1ogs_A-2wnw_A.png|thumb|150px|2wnw_A]]
  +
|[[File:modeller-hhsearch-1ogs_A-2y24_A.png|thumb|150px|2y24_A]]
  +
|[[File:modeller-hhsearch-1ogs_A-3nco_A.png|thumb|150px|3nco_A]]
  +
|[[File:modeller-hhsearch-dope.png|thumb|200px|Dope score per residue.]]
  +
|}
  +
  +
<figtable id="tab:modeller-hhsearch-results">
  +
{| style="border-collapse: separate; border-style: solid; border-spacing: 0; border-width: 2px 0 2px 0; text-align:right" width="700px"
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|- style="background-color: lightgrey; height=0"
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! style="border-style:solid; border-width: 0 1px 0 0" | Template
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! DOPE
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! DOPE z-score
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! style="border-style:solid; border-width: 0 1px 0 0" | QMEAN6
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! RMSD
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! TM-score
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! GDT_TS
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! GTD_HA
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|-
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| style="border-style:solid; border-width: 1px 0 0 0" colspan=8|
  +
|-
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|style="border-style:solid; border-width: 0 1px 0 0" | 2wnw_A
  +
| -54695
  +
| -0.295
  +
| style="border-style:solid; border-width: 0 1px 0 0" | 0.689
  +
| 1.079
  +
| 0.869
  +
| 0.732
  +
| 0.538
  +
|-
  +
|style="border-style:solid; border-width: 0 1px 0 0" | 2y24_A
  +
| -47256
  +
| 0.765
  +
| style="border-style:solid; border-width: 0 1px 0 0" | 0.376
  +
| 1.640
  +
| 0.722
  +
| 0.553
  +
| 0.386
  +
|-
  +
|style="border-style:solid; border-width: 0 1px 0 0" | 3nco_A
  +
| -32577
  +
| 2.857
  +
| style="border-style:solid; border-width: 0 1px 0 0" | 0.139
  +
| 9.757
  +
| 0.398
  +
| 0.235
  +
| 0.131
 
|}
  
|}
 
</figtable>
  
</figtable>

Revision as of 16:00, 29 May 2012

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

2wnw_A
2y24_A
3nco_A
Dope score per residue.

<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

2wnw_A-2y24_A-3kl0_A
2wnw_A-3nco_A
3ik2_A-3nco_A-1egz_A
Dope score per residue.

<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 HHsearch alignments

2wnw_A
2y24_A
3nco_A
2wnw_A
2y24_A
3nco_A
Dope score per residue.

<figtable id="tab:modeller-hhsearch-results">

Template DOPE DOPE z-score QMEAN6 RMSD TM-score GDT_TS GTD_HA
2wnw_A -54695 -0.295 0.689 1.079 0.869 0.732 0.538
2y24_A -47256 0.765 0.376 1.640 0.722 0.553 0.386
3nco_A -32577 2.857 0.139 9.757 0.398 0.235 0.131

</figtable>

SWISS-MODEL

Automated mode

2wnw_A
2y24_A
3nco_A
Dope score per residue.

<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

2wnw_A
2y24_A
3nco_A
Dope score per residue.

<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>

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