10 Free Software for protein 3D structure visualization

In some of my previous posts, I was talking about protein 3D structure modelling. I discussed the basics of protein structure and different methods of protein modelling. You can read them here:

But building a protein structure is not enough you have to visualize your final protein tertiary structure to analyze the result. There are so many good software to visualize the protein structure. here I am giving the list of some of the best and most widely used tools of protein 3D structure visualization
  1. BioBlender
  2. Visual Molecular Dynamics : can be use for modeling, visualization, and analysis of biological systems such as proteins, nucleic acids, lipid bilayer assemblies. VMD have so many other functions also beside protein structure visualization.
  3. Jmol
  4. PyMOL
  5. RasMol
  6. UCSF Chimera :  can be used for 'interactive visualization and analysis of molecular structures and related data, including density maps, supramolecular assemblies, sequence alignments, docking results, trajectories, and conformational ensembles'
  7. Friend
  8. VisProt3DS 
  9. Polyview-3D : A web server and good point to start with if you don't like to install any software on your computer.
  10. Swiss pdb viewer : My favorite one. Very light and can work very efficiently. Please watch this beautiful bioinformatic video tutorial to learn to use Swiss pdb viewer. Even you can use  Swiss pdb viewer along with SWISS-MODEL for protein homology modeling. You can vier this free  bioinformatic video tutorial for detail


  1. Many thanks for this summary - was very useful in helping me to better understand the options that are available.

  2. Hi,

    Would you happen to know how one creates a beautiful image of a protein such as the ones shown on the "Protein of the Month" page on the PDB website? For example this image: http://www.rcsb.org/pdb/education_discussion/molecule_of_the_month/images/ATPsynthase-icon.gif

    I tried in Pymol, but it didn't work. It seems like the author uses Rasmol to visualize his proteins. Is there an option in Rasmol to do that?

    Thank you!

    1. Pymol is a strong protein structure visualization tool. They have several options and you can download several script from their website too. Actually it's my personal favorite. All you have to do is to explore it properly. Even Chimera is my second favorite. However this image seems to generated by rasmol.

  3. Hello.
    Thank you for the blog. I was wondering how I should use the modelling tools if my protein does not have a PDB entry?


  4. Hello,
    Thank you for the helpful blog! I was wondering how to use these modelling softwares when my protein does not have a PDB ID?


    1. Hi,
      I think in that case you can use the ab inItio method. That is described HERE

  5. What are the most powerful software for the prediction of epitopes and the modeling of the 3D structure of proteins ?

  6. What are the most powerful software for the prediction of epitopes and the modeling of the 3D structure of proteins ?


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