Difference between revisions of "Fabry:Structure-based mutation analysis"

From Bioinformatikpedia
(Created page with " == Preparation == Before we start you will have to choose one of structures available == Vizualisation == Map all the 10 mutations onto the crystal structure. == Create mu…")
 
(→‎Preparation)
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== Preparation ==
  
== Preparation ==
  +
<div style="float:left; border:thin solid lightgrey; margin: 0px 0px 0px 0px;">
−  
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<figtable id="tab:XXX">
−
Before we start you will have to choose one of structures available
 
  +
<caption>ADD CAPTION HERE</caption>
  +
{| class="wikitable sortable" style="border-collapse: collapse; border-spacing: 0; border-width: 1px; border-style: solid; padding-left:5px; padding-right:5px; border-color: #000; padding: 0"
  +
! style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 2px 0;"| Entry
  +
! style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 2px 0;"| Method
  +
! style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 2px 0;"| Resolution (Å)
  +
! style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 2px 0;"| Chain
  +
! style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 2px 0;"| Positions
  +
! style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 2px 0;"| PDBsum
  +
! style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 2px 0;"| PDB
  +
! style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 2px 0;"| R-factor
  +
|-
  +
| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| 1R46
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| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| X-ray
  +
| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| 3.25
  +
| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| A/B
  +
| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| 32-429
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| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| [http://www.ebi.ac.uk/pdbsum/1R46 [»]]
  +
| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| [http://www.pdb.org/pdb/explore/explore.do?structureId=1R46 [»]]
  +
| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| 0.262
  +
|-
  +
| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| 1R47
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| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| X-ray
  +
| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| 3.45
  +
| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| A/B
  +
| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| 32-429
  +
| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| [http://www.ebi.ac.uk/pdbsum/1R47 [»]]
  +
| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| [http://www.pdb.org/pdb/explore/explore.do?structureId=1R47 [»]]
  +
| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| 0.285
  +
|-
  +
| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| 3GXN
  +
| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| X-ray
  +
| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| 3.01
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| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| A/B
  +
| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| 32-429
  +
| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| [http://www.ebi.ac.uk/pdbsum/3GXN [»]]
  +
| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| [http://www.pdb.org/pdb/explore/explore.do?structureId=3GXN [»]]
  +
| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| 0.239
  +
|-
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| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| 3GXP
  +
| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| X-ray
  +
| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| 2.20
  +
| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| A/B
  +
| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| 32-429
  +
| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| [http://www.ebi.ac.uk/pdbsum/3GXP [»]]
  +
| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| [http://www.pdb.org/pdb/explore/explore.do?structureId=3GXP [»]]
  +
| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| 0.204
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|-
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| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| 3GXT
  +
| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| X-ray
  +
| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| 2.70
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| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| A/B
  +
| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| 32-429
  +
| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| [http://www.ebi.ac.uk/pdbsum/3GXT [»]]
  +
| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| [http://www.pdb.org/pdb/explore/explore.do?structureId=3GXT [»]]
  +
| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| 0.245
  +
|-
  +
| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| 3HG2
  +
| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| X-ray
  +
| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| 2.30
  +
| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| A/B
  +
| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| 32-429
  +
| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| [http://www.ebi.ac.uk/pdbsum/3HG2 [»]]
  +
| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| [http://www.pdb.org/pdb/explore/explore.do?structureId=3HG2 [»]]
  +
| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| 0.178
  +
|-
  +
| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0; color: #A1C820; border-color: black"| 3HG3
  +
| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0; color: #A1C820; border-color: black"| X-ray
  +
| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0; color: #A1C820; border-color: black"| 1.90
  +
| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0; color: #A1C820; border-color: black"| A/B
  +
| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0; color: #A1C820; border-color: black"| 32-429
  +
| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0; "| [http://www.ebi.ac.uk/pdbsum/3HG3 [»]]
  +
| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0; "| [http://www.pdb.org/pdb/explore/explore.do?structureId=3HG3 [»]]
  +
| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0; color: #A1C820; border-color: black"| 0.167
  +
|-
  +
| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| 3HG4
  +
| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| X-ray
  +
| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| 2.30
  +
| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| A/B
  +
| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| 32-429
  +
| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| [http://www.ebi.ac.uk/pdbsum/3HG4 [»]]
  +
| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| [http://www.pdb.org/pdb/explore/explore.do?structureId=3HG4 [»]]
  +
| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| 0.166
  +
|-
  +
| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| 3HG5
  +
| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| X-ray
  +
| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| 2.30
  +
| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| A/B
  +
| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| 32-429
  +
| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| [http://www.ebi.ac.uk/pdbsum/3HG5 [»]]
  +
| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| [http://www.pdb.org/pdb/explore/explore.do?structureId=3HG5 [»]]
  +
| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| 0.192
  +
|-
  +
| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| 3LX9
  +
| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| X-ray
  +
| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| 2.04
  +
| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| A/B
  +
| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| 32-429
  +
| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| [http://www.ebi.ac.uk/pdbsum/3LX9 [»]]
  +
| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| [http://www.pdb.org/pdb/explore/explore.do?structureId=3LX9 [»]]
  +
| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| 0.178
  +
|-
  +
| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| 3LXA
  +
| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| X-ray
  +
| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| 3.04
  +
| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| A/B
  +
| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| 32-429
  +
| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| [http://www.ebi.ac.uk/pdbsum/3LXA [»]]
  +
| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| [http://www.pdb.org/pdb/explore/explore.do?structureId=3LXA [»]]
  +
| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| 0.216
  +
|-
  +
| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| 3LXB
  +
| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| X-ray
  +
| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| 2.85
  +
| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| A/B
  +
| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| 32-429
  +
| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| [http://www.ebi.ac.uk/pdbsum/3LXB [»]]
  +
| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| [http://www.pdb.org/pdb/explore/explore.do?structureId=3LXB [»]]
  +
| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| 0.227
  +
|-
  +
| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| 3LXC
  +
| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| X-ray
  +
| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| 2.35
  +
| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| A/B
  +
| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| 32-429
  +
| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| [http://www.ebi.ac.uk/pdbsum/3LXC [»]]
  +
| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| [http://www.pdb.org/pdb/explore/explore.do?structureId=3LXC [»]]
  +
| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| 0.186
  +
|-
  +
| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| 3S5Y
  +
| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| X-ray
  +
| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| 2.10
  +
| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| A/B
  +
| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| 32-429
  +
| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| [http://www.ebi.ac.uk/pdbsum/3S5Y [»]]
  +
| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| [http://www.pdb.org/pdb/explore/explore.do?structureId=3S5Y [»]]
  +
| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| 0.195
  +
|-
  +
| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| 3S5Z
  +
| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| X-ray
  +
| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| 2.00
  +
| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| A/B
  +
| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| 32-429
  +
| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| [http://www.ebi.ac.uk/pdbsum/3S5Z [»]]
  +
| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| [http://www.pdb.org/pdb/explore/explore.do?structureId=3S5Z [»]]
  +
| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| 0.211
  +
|-
  +
| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| 3TV8
  +
| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| X-ray
  +
| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| 2.64
  +
| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| A/B
  +
| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| 32-429
  +
| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| [http://www.ebi.ac.uk/pdbsum/3TV8 [»]]
  +
| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| [http://www.pdb.org/pdb/explore/explore.do?structureId=3TV8 [»]]
  +
| style="border-style: solid; padding-left:5px; padding-right:5px; border-width: 0 1px 1px 0;"| 0.203
  +
|-
  +
|}
  +
</figtable>
  +
</div>
  +
<br style="clear:both">
   
 
== Vizualisation ==
  
== Vizualisation ==

Revision as of 08:44, 20 June 2012

Preparation

<figtable id="tab:XXX"> ADD CAPTION HERE

Entry Method Resolution (Å) Chain Positions PDBsum PDB R-factor
1R46 X-ray 3.25 A/B 32-429 [»] [»] 0.262
1R47 X-ray 3.45 A/B 32-429 [»] [»] 0.285
3GXN X-ray 3.01 A/B 32-429 [»] [»] 0.239
3GXP X-ray 2.20 A/B 32-429 [»] [»] 0.204
3GXT X-ray 2.70 A/B 32-429 [»] [»] 0.245
3HG2 X-ray 2.30 A/B 32-429 [»] [»] 0.178
3HG3 X-ray 1.90 A/B 32-429 [»] [»] 0.167
3HG4 X-ray 2.30 A/B 32-429 [»] [»] 0.166
3HG5 X-ray 2.30 A/B 32-429 [»] [»] 0.192
3LX9 X-ray 2.04 A/B 32-429 [»] [»] 0.178
3LXA X-ray 3.04 A/B 32-429 [»] [»] 0.216
3LXB X-ray 2.85 A/B 32-429 [»] [»] 0.227
3LXC X-ray 2.35 A/B 32-429 [»] [»] 0.186
3S5Y X-ray 2.10 A/B 32-429 [»] [»] 0.195
3S5Z X-ray 2.00 A/B 32-429 [»] [»] 0.211
3TV8 X-ray 2.64 A/B 32-429 [»] [»] 0.203

</figtable>


Vizualisation

Map all the 10 mutations onto the crystal structure.


Create mutation

SCWRL


Comparison energies

foldX

Minimise

Gromacs

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