Difference between revisions of "Canavan Disease: Task 09 - Supplement"

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==FoldX==
  
==FoldX==
  +
  +
Complete and detailed energy calculation output by foldX
  +
 
<figtable id="foldX">
  
<figtable id="foldX">
 
{| border="1" cellpadding="5" cellspacing="0" align="center" style="text-align:center"
  
{| border="1" cellpadding="5" cellspacing="0" align="center" style="text-align:center"
 
|-
  
|-
−
! colspan="23" style="background:#87CEFA;" width="500"| foldX Result List
+
! colspan="11" style="background:#87CEFA;" width="500"| foldX Result List
 
|-
  
|-
 
! style="background:#BFBFBF;" align="center"| Mutation
  
! style="background:#BFBFBF;" align="center"| Mutation
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! style="background:#BFBFBF;" align="center"| Entropy Sidechain
 
! style="background:#BFBFBF;" align="center"| Entropy Sidechain
 
! style="background:#BFBFBF;" align="center"| Entropy Mainchain
 
! style="background:#BFBFBF;" align="center"| Entropy Mainchain
  +
|-
  +
|Wildtype || 144.46 || -348.85 || -111.78 || -750.45 || -36.46 || 985.82 || -998.14 || 75.54 || 374.56 || 930.45
  +
|-
  +
|Asn121Asp || 145.46 || -348.38 || -112.53 || -750.20 || -35.65 || 987.17 || -998.00 || 75.59 || 373.86 || 929.57
  +
|-
  +
|His21Pro || 145.85 || -349.14 || -110.89 || -748.05 || -35.60 || 980.22 || -997.07 || 73.77 || 372.49 || 931.09
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|-
  +
|Pro149Ala || 148.04 || -348.85 || -111.78 || -750.34 || -36.46 || 987.21 || -998.03 || 74.87 || 374.16 || 930.76
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|-
  +
|Pro257Arg || 149.63 || -349.67 || -112.74 || -750.59 || -36.69 || 988.68 || -997.85 || 75.54 || 375.35 || 931.92
  +
|-
  +
|Thr166Ile || 147.35 || -347.52 || -112.78 || -751.45 || -36.74 || 988.51 || -1000.35 || 78.16 || 374.57 || 929.25
  +
|-
  +
|}
  +
</figtable>
  +
  +
  +
<figtable id="foldX2">
  +
{| border="1" cellpadding="5" cellspacing="0" align="center" style="text-align:center"
  +
|-
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! colspan="13" style="background:#87CEFA;" width="500"| foldX Result List
  +
|-
  +
! style="background:#BFBFBF;" align="center"| Mutation
 
! style="background:#BFBFBF;" align="center"| Sloop_Entropy
 
! style="background:#BFBFBF;" align="center"| Sloop_Entropy
 
! style="background:#BFBFBF;" align="center"| Mloop_Entropy
 
! style="background:#BFBFBF;" align="center"| Mloop_Entropy
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! style="background:#BFBFBF;" align="center"| Entropy Complex
 
! style="background:#BFBFBF;" align="center"| Entropy Complex
 
|-
  
|-
−
|Wildtype || 144.46 || -348.85 || -111.78 || -750.45 || -36.46 || 985.82 || -998.14 || 75.54 || 374.56 || 930.45 || 0.00 || 0.00 || 8.08 || 53.11 || 357.94 || -3.05 || -6.28 || 0.00 || -1.13 || -29.63 || 2.66 || 0.00
 +
|Wildtype || 0.00 || 0.00 || 8.08 || 53.11 || 357.94 || -3.05 || -6.28 || 0.00 || -1.13 || -29.63 || 2.66 || 0.00
 
|-
  
|-
−
|Asn121Asp || 145.46 || -348.38 || -112.53 || -750.20 || -35.65 || 987.17 || -998.00 || 75.59 || 373.86 || 929.57 || 0.00 || 0.00 || 8.08 || 51.67 || 357.74 || -3.13 || -4.45 || 0.00 || -1.17 || -29.63 || 2.66 || 0.00
 +
|Asn121Asp || 0.00 || 0.00 || 8.08 || 51.67 || 357.74 || -3.13 || -4.45 || 0.00 || -1.17 || -29.63 || 2.66 || 0.00
 
|-
  
|-
−
|His21Pro || 145.85 || -349.14 || -110.89 || -748.05 || -35.60 || 980.22 || -997.07 || 73.77 || 372.49 || 931.09 || 0.00 || 0.00 || 8.08 || 52.01 || 356.94 || -3.02 || -5.11 || 0.00 || -1.13 || -24.30 || 2.51 || 0.00
 +
|His21Pro || 0.00 || 0.00 || 8.08 || 52.01 || 356.94 || -3.02 || -5.11 || 0.00 || -1.13 || -24.30 || 2.51 || 0.00
 
|-
  
|-
−
|Pro149Ala || 148.04 || -348.85 || -111.78 || -750.34 || -36.46 || 987.21 || -998.03 || 74.87 || 374.16 || 930.76 || 0.00 || 0.00 || 6.95 || 55.14 || 358.44 || -3.05 || -4.45 || 0.00 || -1.13 || -29.63 || 2.66 || 0.00
 +
|Pro149Ala || 0.00 || 0.00 || 6.95 || 55.14 || 358.44 || -3.05 || -4.45 || 0.00 || -1.13 || -29.63 || 2.66 || 0.00
 
|-
  
|-
−
|Pro257Arg || 149.63 || -349.67 || -112.74 || -750.59 || -36.69 || 988.68 || -997.85 || 75.54 || 375.35 || 931.92 || 0.00 || 0.00 || 8.08 || 53.22 || 358.75 || -3.05 || -4.45 || 0.00 || -1.13 || -29.63 || 2.66 || 0.00
 +
|Pro257Arg || 0.00 || 0.00 || 8.08 || 53.22 || 358.75 || -3.05 || -4.45 || 0.00 || -1.13 || -29.63 || 2.66 || 0.00
 
|-
  
|-
−
|Thr166Ile || 147.35 || -347.52 || -112.78 || -751.45 || -36.74 || 988.51 || -1000.35 || 78.16 || 374.57 || 929.25 || 0.00 || 0.00 || 8.08 || 53.22 || 357.95 || -3.05 || -4.45 || 0.00 || -1.13 || -29.63 || 2.67 || 0.00
 +
|Thr166Ile || 0.00 || 0.00 || 8.08 || 53.22 || 357.95 || -3.05 || -4.45 || 0.00 || -1.13 || -29.63 || 2.67 || 0.00
 
|-
  
|-
 
|}
  
|}
−
<center><small>'''<caption>''' foldX results </caption></small></center>
  
 
</figtable>
  
</figtable>
   
  +
==Minimization==
   
  +
Exact numbers used to create the energy development plot:
   
−
==Minimization==
  
 
<figtable id="energy_comp">
  
<figtable id="energy_comp">
 
{| border="1" cellpadding="5" cellspacing="0" align="center" style="text-align:center"
  
{| border="1" cellpadding="5" cellspacing="0" align="center" style="text-align:center"
 
|-
  
|-
−
! colspan="6" style="background:#87CEFA;" width="500"| Minimization of foldX structures
+
! colspan="6" style="background:#87CEFA;" width="500"| Minimization of foldX Structures
 
|-
  
|-
 
! rowspan="2" style="background:#BFBFBF;"| Mutation
  
! rowspan="2" style="background:#BFBFBF;"| Mutation

Latest revision as of 19:18, 4 September 2013

Link back to Task 09: Structure-based Mutation Analysis

FoldX

Complete and detailed energy calculation output by foldX

<figtable id="foldX">

foldX Result List
Mutation Total Energy Backbone Hbond Sidechain Hbond Van der Waals Electrostatics Solvation Polar Solvation Hydrophobic Van der Waals Clashes Entropy Sidechain Entropy Mainchain
Wildtype 144.46 -348.85 -111.78 -750.45 -36.46 985.82 -998.14 75.54 374.56 930.45
Asn121Asp 145.46 -348.38 -112.53 -750.20 -35.65 987.17 -998.00 75.59 373.86 929.57
His21Pro 145.85 -349.14 -110.89 -748.05 -35.60 980.22 -997.07 73.77 372.49 931.09
Pro149Ala 148.04 -348.85 -111.78 -750.34 -36.46 987.21 -998.03 74.87 374.16 930.76
Pro257Arg 149.63 -349.67 -112.74 -750.59 -36.69 988.68 -997.85 75.54 375.35 931.92
Thr166Ile 147.35 -347.52 -112.78 -751.45 -36.74 988.51 -1000.35 78.16 374.57 929.25

</figtable>


<figtable id="foldX2">

foldX Result List
Mutation Sloop_Entropy Mloop_Entropy Cis_Bond Torsional Clash Backbone Clash Helix Dipole Water Bridge Disulfide Electrostatic Kon Partial Covalent Bonds Energy Ionisation Entropy Complex
Wildtype 0.00 0.00 8.08 53.11 357.94 -3.05 -6.28 0.00 -1.13 -29.63 2.66 0.00
Asn121Asp 0.00 0.00 8.08 51.67 357.74 -3.13 -4.45 0.00 -1.17 -29.63 2.66 0.00
His21Pro 0.00 0.00 8.08 52.01 356.94 -3.02 -5.11 0.00 -1.13 -24.30 2.51 0.00
Pro149Ala 0.00 0.00 6.95 55.14 358.44 -3.05 -4.45 0.00 -1.13 -29.63 2.66 0.00
Pro257Arg 0.00 0.00 8.08 53.22 358.75 -3.05 -4.45 0.00 -1.13 -29.63 2.66 0.00
Thr166Ile 0.00 0.00 8.08 53.22 357.95 -3.05 -4.45 0.00 -1.13 -29.63 2.67 0.00

</figtable>

Minimization

Exact numbers used to create the energy development plot:

<figtable id="energy_comp">

Minimization of foldX Structures
Mutation Iteration
#1 #2 #3 #4 #5
Wildtype -15030 -15133 -14690 -14689 -14445
Asn121Asp -14958 -15062 -14610 -14617 -14391
His21Pro -14962 -15069 -14624 -14624 -14389
Pro129Ala -15049 -15148 -14708 -14712 -14468
Pro257Arg -14991 -15094 -14644 -14648 -14406
Thr166Ile -14128 -15026 -14711 -14290 -14301
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