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Instant-use add-on functions for the Wolfram Language

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 BioSequenceMoleculePlot3D

Source Notebook

Visualize a biomolecular sequence in 3D with highlighted residues

Contributed by: Jan Mangaldan

ResourceFunction["BioSequenceMoleculePlot3D"][bioseq]

creates a three-dimensional model of the biomolecular sequence bioseq, where all residues are highlighted.

Details and Options

If bioseq is a BioSequence of type "Peptide" or "CircularPeptide", individual amino acids comprising the peptide are highlighted.
If bioseq is a BioSequence of type "DNA", "RNA", "CircularDNA" or "CircularRNA", individual nucleobases are highlighted.
Hybrid strands and sequence collections are supported.
ResourceFunction["BioSequenceMoleculePlot3D"] returns a Graphics3D expression.
ResourceFunction["BioSequenceMoleculePlot3D"] has the same options as MoleculePlot3D, with the following additions:
"Highlighting"Automatichow to highlight the given BioSequence
With "Highlighting"→"ResidueSugar", the phosphate groups and sugars in DNA and RNA sequences are highlighted separately. With "Highlighting"→"ResidueBackbone", the phosphate groups and sugars are highlighted with a single color.

Examples

Basic Examples (1) 

Visualize the structure of the "beefy meaty peptide":

In[1]:=
ResourceFunction["BioSequenceMoleculePlot3D"][ BioSequence["Peptide", "KGDEESLA"]]
Out[1]=

Scope (2) 

Visualize the structure of the circular peptide evolidine:

In[2]:=
ResourceFunction["BioSequenceMoleculePlot3D"][ BioSequence["CircularPeptide", "SFLPVNL"]]
Out[2]=

Compare an RNA and a circular RNA sequence:

In[3]:=
{ResourceFunction["BioSequenceMoleculePlot3D"][ BioSequence["RNA", "AUCG"]], ResourceFunction["BioSequenceMoleculePlot3D"][ BioSequence["CircularRNA", "AUCG"]]} // GraphicsRow
Out[3]=

Options (2) 

Highlighting (2) 

Highlight the sugars and phosphate groups together in a DNA-RNA hybrid strand:

In[4]:=
ResourceFunction["BioSequenceMoleculePlot3D"][ BioSequence[ "HybridStrand", {BioSequence["DNA", "TGC"], BioSequence["RNA", "GUA"]}], "Highlighting" -> "ResidueBackbone"]
Out[4]=

Highlight the sugars and phosphate groups separately:

In[5]:=
ResourceFunction["BioSequenceMoleculePlot3D"][ BioSequence[ "HybridStrand", {BioSequence["DNA", "TGC"], BioSequence["RNA", "GUA"]}], "Highlighting" -> "ResidueSugar"]
Out[5]=

Neat Examples (1) 

Highlight the amino acid residues in robustoxin, a component of the venom of the spider Atrax robustus:

In[6]:=
ResourceFunction["BioSequenceMoleculePlot3D"][ BioSequence["CAKKRNWCGKNEDCCCPMKCIYAWYNQQGSCQTTITGLFKKC", Bond /@ {{1, 15}, {8, 20}, {14, 31}, {16, 42}}]]
Out[6]=

Version History

  • 1.0.0 – 31 January 2022

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