Blending Proteins

Democratising access to beautiful molecular landscapes.

Brady Johnston (@bradyajohnston)

Traditional Flow of Structural Data

  • Data exists in .pdb or other structure file
ATOM      1  N   ASP A   1      42.099  12.935 -17.274  1.00 43.88      A    N  
ATOM      2  CA  ASP A   1      40.682  12.606 -17.121  1.00 55.80      A    C  
ATOM      3  C   ASP A   1      40.605  12.058 -15.711  1.00 57.97      A    C  
ATOM      4  O   ASP A   1      41.631  11.916 -15.024  1.00 64.28      A    O  
ATOM      5  CB  ASP A   1      40.272  11.534 -18.141  1.00 63.10      A    C  
ATOM      6  CG  ASP A   1      41.162  10.287 -18.062  1.00 59.15      A    C  
ATOM      7  OD1 ASP A   1      41.296   9.672 -16.981  1.00 64.73      A    O  
ATOM      8  OD2 ASP A   1      41.775   9.965 -19.091  1.00 76.58      A    O  
ATOM      9  N   VAL A   2      39.394  11.714 -15.302  1.00 59.57      A    N  
ATOM     10  CA  VAL A   2      39.137  11.285 -13.940  1.00 60.76      A    C
  • Loaded in to software like PyMol, ChimeraX
    • Data is translated to 3D geometry for visualisation

More ‘Cinematic’ Visulisations

  • Export 3D geometry to other dedicated 3D programs (Blender, Maya)
  • Connection to underlying scientific data is lost

Protein Motor Goes brrrrrrrrrr

  • Cinematic visualisation of structural data
    • Bacterial Flagellar (7CG0)











  • Computationally heavy to export from ChimeraX
    • .pdb file is only ~ 100 MB
    • 3D model file is ~ 10 GB
    • 55 GB RAM & 40 minutes required to import model into Blender

Molecular Dynamics

Instancing of Single Proteins

Biological Assemblies

Molecular Landscapes

Automatic Creation of DNA?

Automatic Animation of DNA?

Incorporate with .pdb Structures

Animating Static Crystal Structures

Animating Amino Acids

Who Needs AlphaFold?

Animating Static Viral Assemblies

Molecular Nodes

  • Free and open source

  • ‘Relatively’ easy to use

  • Import and Animate:

    • Static PDB structures
    • Molecluar dynamics trajectories (via MDAnalysis)
    • Multi-state .pdb files from a structural morph
    • bio-polymers (DNA, peptides, actin filaments etc)

Scan to find out more!

@bradyajohnston