We can easily get an amino acid and see its molecule in 2D or 3D
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MoleculeName[#],MoleculePlot#,,MoleculePlot3D#,&/@RandomChoiceEntityList,1//Grid
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(2R)-2-amino-3-sulfanylpropanoic acid |  |
We can define a pattern and highlight it. Let’s show the amino and carboxylic acid.
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With{amino=Molecule[{"N","H","H"},{Bond[{1,2},"Single"],Bond[{1,3},"Single"]}],carboxylicacid=Molecule[{"C","O","O","H"},{Bond[{1,2},"Double"],Bond[{1,3},"Single"],Bond[{3,4},"Single"]}]},MoleculePlot#1,Association["amino"amino,"carboxylic acid"carboxylicacid],,,MoleculePlot3D#1,Association["amino"amino,"carboxylic acid"carboxylicacid],&/@//
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We can define the peptide bond and bond two amino acids.
(Except for proline and glutamine. These are “special”).
(Except for proline and glutamine. These are “special”).
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,,,,,,,,,,,,,,,,,
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WithpeptideBond=MoleculePattern{"C","O","N","H",Atom[Except["H"]]},,nhhcooh=MoleculePattern{"N","H","H","C","O","O","H"},,peptide=MoleculePattern{"N","H","H","C","O","N","H","C","O","O","H"},,water=MoleculePattern{"H","H","O"},,proteinSynthesis=PatternReaction{nhhcooh,nhhcooh}->{peptide,water},;MoleculePlotApplyReactionproteinSynthesis,,1,,peptideBond,
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Now that we have defined the reaction for peptide bind formation, we can chain amino acids together into a polypeptide.
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