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ProteinVisualization

Guides

  • Protein Visualization

Symbols

  • AlphaCarbonPathPlot3D
  • AmidePlanePlot
  • AMPathogenicity
  • BiomoleculePlot3D
  • DihedralAnglePlot
  • ExtractBackboneCoordinates
  • MissenseVariantArrayPlot
  • MissenseVariantData
  • MissenseVariantListPlot
  • MissenseVariantPlot3D
  • MissenseVariantSubstitutionMatrixPlot
  • PathogenicityConfidenceCorrelation
  • PathogenicityConfidencePlot
  • ProteinBackboneAtomPlot
  • ProteinContactGraphPlot
  • ProteinContactMap
  • RamachandranAngles
  • RamachandranPlot
  • ResidueDistanceGraph
  • ResidueDistanceMatrix
  • $CrystalStructuresDirectory
WolframChemistry`ProteinVisualization`
ExtractBackboneCoordinates
​
ExtractBackboneCoordinates
[biomol]
returns the coordinates of α-carbon atoms in protein chains and O3' atoms in nucleic acid chains.
​
Details and Options

Examples  
(10)
Basic Examples  
(1)
Compute the backbone coordinates of avian pancreatic polypeptide : Small globular protein hormone :
In[1]:=
ExtractBackboneCoordinates
["1PPT"]
Out[1]=
{{{1.47,-9.017,17.255},{-1.135,-10.606,14.958},{-0.626,-14.187,14.053},{0.489,-14.94,10.481},{-2.414,-14.97,8.087},{-3.548,-18.158,6.308},{-3.065,-18.017,2.495},{-6.566,-18.626,0.996},{-5.423,-20.73,-1.983},{-4.521,-19.865,-5.611},{-8.106,-20.411,-6.537},{-9.622,-18.132,-4.017},{-11.981,-15.406,-5.466},{-10.341,-11.949,-5.914},{-12.142,-10.553,-2.855},{-10.488,-13.19,-0.722},{-7.028,-12.438,-2.126},{-7.676,-8.682,-1.354},{-8.636,-9.644,2.284},{-5.441,-11.78,2.548},{-3.402,-8.885,1.007},{-4.728,-6.473,3.688},{-4.038,-8.947,6.542},{-0.451,-9.679,5.213},{0.085,-5.877,5.096},{-0.856,-5.563,8.757},{1.356,-8.52,9.698},{4.342,-7.279,7.784},{4.064,-3.735,9.328},{4.069,-5.352,12.824},{7.001,-7.699,12.162},{9.068,-4.861,10.736},{7.995,-2.499,13.658},{6.779,0.039,11.099},{3.108,0.616,11.852},{2.765,3.446,9.296}}}
Scope  
(8)

Applications  
(1)

SeeAlso
ProteinBackboneAtomPlot
 
▪
$CrystalStructuresDirectory
RelatedGuides
▪
Protein Visualization
RelatedLinks
▪
Protein Structure Database
▪
α-Carbon for amino acids
▪
ESMFold
▪
AlphaFold Protein Structure Database
▪
ESMAtlas
""

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