Two Packages, One Goal

The first package is called Bio3D, which focuses on the biological information being transmitted in a form of a data table that R can then read and work with.

The second package, R3DMOL, is used to create 3D visualizations of many molecular biological objects.

Together, they let me take biological data, load it into R, and then turn it into clear and colorful 3D models.

The main functions

1. Bio3d: x <- read.pdb(“6VSB”) loads the molecular structure of the COVID spike protein (PDB ID: 6VSB) directly into R.

2. R3dmol: m_add_model(data = x, format = “pdb”) takes the structure already loaded into R and brings it into a 3D format.

3. m_set_style(m_style_cartoon(color = “green”))

The code examples

COVID DNA

COVID spike protein

COVID RNA fragment

Ebola GP protein

Advantages

1.It’s free to use.

2.It’s very easy to work with.

3. It’s a great study and learning tool.

Disadvantages

1. Provides only visualizations.

2. Won’t display interactives in PDF.

Thank you!