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ProteinVisualization

Guides

  • Protein Visualization

Symbols

  • AlphaCarbonPathPlot3D
  • AmidePlanePlot
  • BiomoleculePlot3D
  • DihedralAnglePlot
  • ExtractBackboneCoordinates
  • ProteinBackboneAtomPlot
  • ProteinContactGraphPlot
  • ProteinContactMap
  • RamachandranAngles
  • RamachandranPlot
  • ResidueDistanceGraph
  • ResidueDistanceMatrix
  • $CrystalStructuresDirectory
WolframChemistry`ProteinVisualization`
ExtractBackboneCoordinates
​
ExtractBackboneCoordinates
[biomol]
returns the coordinates of α-carbon atoms in protein chains and phosphorus atoms in nucleic acid chains.
​
Details and Options

Examples  
(8)
Basic Examples  
(1)
Compute the backbone coordinates of avian pancreatic polypeptide : Small globular protein hormone :
In[1]:=
ExtractBackboneCoordinates
["1PPT"]
Out[1]=
{{{147.,-901.7,1725.5},{-113.5,-1060.6,1495.8},{-62.6,-1418.7,1405.3},{48.9,-1494.,1048.1},{-241.4,-1497.,808.7},{-354.8,-1815.8,630.8},{-306.5,-1801.7,249.5},{-656.6,-1862.6,99.6},{-542.3,-2073.,-198.3},{-452.1,-1986.5,-561.1},{-810.6,-2041.1,-653.7},{-962.2,-1813.2,-401.7},{-1198.1,-1540.6,-546.6},{-1034.1,-1194.9,-591.4},{-1214.2,-1055.3,-285.5},{-1048.8,-1319.,-72.2},{-702.8,-1243.8,-212.6},{-767.6,-868.2,-135.4},{-863.6,-964.4,228.4},{-544.1,-1178.,254.8},{-340.2,-888.5,100.7},{-472.8,-647.3,368.8},{-403.8,-894.7,654.2},{-45.1,-967.9,521.3},{8.5,-587.7,509.6},{-85.6,-556.3,875.7},{135.6,-852.,969.8},{434.2,-727.9,778.4},{406.4,-373.5,932.8},{406.9,-535.2,1282.4},{700.1,-769.9,1216.2},{906.8,-486.1,1073.6},{799.5,-249.9,1365.8},{677.9,3.9,1109.9},{310.8,61.6,1185.2},{276.5,344.6,929.6}}}
Scope  
(6)

Applications  
(1)

SeeAlso
ProteinBackboneAtomPlot
 
▪
$CrystalStructuresDirectory
RelatedGuides
▪
Protein Visualization
RelatedLinks
▪
Protein Structure Database
▪
α-Carbon for amino acids
▪
ESMFold
""

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