Wolfram Function Repository

Instant-use add-on functions for the Wolfram Language

Function Repository Resource:

 PeptideName

Source Notebook

Construct the semisystematic name of a peptide from its amino acid sequence

Contributed by: Jan Mangaldan

ResourceFunction["PeptideName"]["seq"]

gives the semisystematic name of the peptide corresponding to the sequence string "seq".

ResourceFunction["PeptideName"][expr]

gives the semisystematic name of the peptide represented by expr.

Details and Options

The sequence string "seq" is assumed to be composed of the one-letter abbreviations for the standard amino acids, as listed in the documentation for BioSequence or the IUPAC-IUB recommendations. This link also describes the semisystematic nomenclature.
expr can be a BioSequence object or an Entity of entity type "Protein".
ResourceFunction["PeptideName"] accepts a "Hyphenate" option that tells whether to insert hyphens in the semisystematic name.

Examples

Basic Examples (1) 

Semisystematic name of the "beefy meaty peptide":

In[1]:=
ResourceFunction["PeptideName"]["KGDEESLA"]
Out[1]=

Scope (4) 

Apply PeptideName to the result of ProteinData:

In[2]:=
ResourceFunction["PeptideName"][ProteinData["SLN"]]
Out[2]=

Show the semisystematic name of a "Protein" Entity:

In[3]:=
ResourceFunction["PeptideName"][Entity["Protein", "OCLM"]]
Out[3]=

Show the semisystematic name of a peptide BioSequence:

In[4]:=
ResourceFunction["PeptideName"][ BioSequence[ "Peptide", "ITGTSTVGVGRGVLGDQKNINTTYSTYYYLQDNTRGNGIFTYDAKYRTTLPGSLWADADNQFF"]]
Out[4]=

Show the semisystematic name of the circular peptide evolidine:

In[5]:=
ResourceFunction["PeptideName"][ BioSequence["CircularPeptide", "SFLPVNL"]]
Out[5]=

Options (1) 

Hyphenate (1) 

Show the hyphenated semisystematic name:

In[6]:=
ResourceFunction["PeptideName"]["SYSMEHFRWGKPVGKKRRPVKVYP", "Hyphenate" -> True]
Out[6]=

Applications (2) 

Convert the result of PeptideName to a Molecule:

In[7]:=
Molecule[ResourceFunction["PeptideName"]["KGDEESLA"]]
Out[7]=

Visualize with MoleculePlot or MoleculePlot3D:

In[8]:=
{MoleculePlot[%], MoleculePlot3D[%]}
Out[8]=

Neat Examples (2) 

Download the amino acid sequence for the protein titin:

Show a portion of the full semisystematic name, reputed to be one of the longest words in the English language:

In[9]:=
Short[titinName = ResourceFunction["PeptideName"][titin]]
Out[9]=
In[10]:=
StringLength[titinName]
Out[10]=

Version History

  • 1.1.0 – 20 December 2021

Source Metadata

  • Citation:
    • IUPAC-IUB Joint Commission on Biochemical Nomenclature (JCBN), "Nomenclature and Symbolism for Amino Acids and Peptides." European Journal of Biochemistry, vol. 138, no. 1, 9–37, 1984. DOI: 10.1111/j.1432-1033.1984.tb07877.x

Related Resources

Author Notes

PeptideName does not currently account for nonstandard amino acids, modified/unusual residues, modified N/C termini, or secondary structure (e.g. disulfide bonds). These will be addressed in a future update.

License Information