Life Sciences
Visualization & Graphics

SARS-CoV-2 Protein Ribbon Diagrams

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Ribbon diagrams are one of the most common ways to visualize protein structures.

Install the ProteinVisualization paclet and load the package:

In[1]:=

PacletInstall["WolframChemistry/ProteinVisualization"];Needs["WolframChemistry`ProteinVisualization`"]

Visualize the structure of SARS-CoV-2 Papain-like protease colored by chains:

In[2]:=

BiomoleculePlot3D"6W9C",

Plot Options



Out[2]=

It is possible to assign custom colors for chains of proteins and specific orientation to view the protein. Here is the structure of SARS-CoV-2 spike protein with custom chain colors and orientation. The input to the function is a four-letter PDB ID unique to a protein structure:

In[3]:=

BiomoleculePlot3D"6VYB","BackboneColorRules""Chains","A"

,"B"

,"C"

,

Plot Options



Out[3]=

A URL can also be used to visualize a specific biological assembly. Here is the structure of biological assembly 1 of the main protease of SARS-CoV-2:

In[4]:=

BiomoleculePlot3D"https://files.rcsb.org/download/6lu7-assembly1.cif.gz",

Plot Options



Out[4]=

Let us create a collection of some important SARS-CoV-2 proteins:

In[5]:=

structureList=MapThreadRasterizeWolframChemistry`ProteinVisualization`BiomoleculePlot3D#1,"BackboneColorRules"{"Chains",#2},

&,

PDB IDs

Chain colors

View Matrices

Protein names

;GraphicsGridPartition[structureList,6],



Out[5]=

External Links

COVID-19/SARS-CoV-2 Resources - RCSB PDB
3D modeling of the SARS-CoV-2 virus in the Wolfram Language

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Citation:
- Lubin, Joseph H., et al. "Evolution of the SARSCoV2 proteome in three dimensions (3D) during the first 6 months of the COVID19 pandemic." Proteins: Structure, Function, and Bioinformatics 90.5 (2022): 1054-1080.

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Contributed by: Soutick Saha

Wolfram Language Example Repository

SARS-CoV-2 Protein Ribbon Diagrams

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