Difference between revisions of "Homology modelling Gaucher Disease"

From Bioinformatikpedia
(→‎Template selection)
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! Template
  
! Template
 
! Identity
  
! Identity
  +
! Query HMM
 
! HHsearch prob
  
! HHsearch prob
 
|-
 
|-
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| colspan=4 style="border-style: solid; border-width: 1px 0 1px 0; font-style: italic; text-align: center;" | > 80% sequence identity
 
| colspan=4 style="border-style: solid; border-width: 1px 0 1px 0; font-style: italic; text-align: center;" | > 80% sequence identity
 
|-
  
|-
−
| style= | 1 || 2nt0_A || 100.0 || 100.0
 +
| style= | 1 || 2nt0_A || 100.0 || 1-497 || 100.0
 
|-
 
|-
 
| colspan=4 style="border-style: solid; border-width: 1px 0 1px 0; font-style: italic; text-align: center;" | 40% - 80% sequence identity
 
| colspan=4 style="border-style: solid; border-width: 1px 0 1px 0; font-style: italic; text-align: center;" | 40% - 80% sequence identity
Line 20: Line 21:
 
|-
  
|-
 
|- style="color:blue; font-weight:bold"
 
|- style="color:blue; font-weight:bold"
−
| 2 || 2wnw_A || 28.0 || 100.0
 +
| 2 || 2wnw_A || 28.0 || 36-496 || 100.0
 
|-
  
|-
−
| 3 || 3clw_A || 14.0 || 100.0
 +
| 3 || 3clw_A || 14.0 || 64-495 || 100.0
 
|- style="color:green; font-weight:bold"
 
|- style="color:green; font-weight:bold"
−
| 4 || 2y24_A || 18.0 || 100.0
 +
| 4 || 2y24_A || 18.0 || 66-495 || 100.0
 
|-
  
|-
−
| 5 || 3kl0_A || 19.0 || 100.0
 +
| 5 || 3kl0_A || 19.0 || 65-495 || 100.0
 
|-
  
|-
−
| 6 || 3zr5_A || 17.0 || 100.0
 +
| 6 || 3zr5_A || 17.0 || 65-494 || 100.0
 
|-
  
|-
−
| 7 || 3ik2_A || 14.0 || 99.2
 +
| 7 || 3ik2_A || 14.0 || 65-495 || 99.2
 
|- style="color:goldenrod; font-weight:bold"
 
|- style="color:goldenrod; font-weight:bold"
−
| 22 || 3nco_A || 11.0 || 97.7
 +
| 22 || 3nco_A || 11.0 || 113-384 || 97.7
 
|-
  
|-
−
| 28 || 1egz_A || 12.0 || 97.4
 +
| 28 || 1egz_A || 12.0 || 113-387 || 97.4
 
|}
  
|}
 
</figtable>
  
</figtable>

Revision as of 14:31, 29 May 2012

Template selection

<figtable id="tab:ss_mapping">

Hit Nr Template Identity Query HMM HHsearch 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>

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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