Depicting Peptides

Problem

You want to depict a molecule as a peptide i.e. a series of amino acid components. See example in Figure 1.

../_images/OEDrawPeptide-Oxytocin.png

Figure 1. Example of depicting oxytocin as a molecule (on the left) and as a peptide (on the right)

Ingredients

  • Grapheme TK - molecule and property visualization toolkit

Note

Requires OpenEye toolkits version 2017.Feb or later.

Difficulty Level

../_images/chilly1.png

Solution

The GraphSim TK provides a function called OEDrawPeptide that depicts a molecule as a peptide. It identifies standard amino acids components in the molecule and substitute them with circular glyphs and their corresponding 3-letter code.

Download code

peptide2img.py and supporting data oxytocin.ism

Usage:

prompt > python3 peptide2img.py oxytocin.ism oxytocin.png

Discussion

The amino acids that are appears naturally in proteins are the L-stereoisomers. These are labeled with corresponding 3-letter codes: such as Ser for L-Serine. Their enantiomers are distinguished by adding the “D-” prefix to their 3-letter code: such as D-Ser for D-Serine.

Table 2. Example of depicting L- and D- Serine
../_images/peptide-L.png ../_images/peptide-D.png

See Also in OEDepict TK Manual

Theory

API

See Also in Grapheme TK Manual

API