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Structure Visualization

It’s generally understood by the molecular biology research community that the sequencing of the human genome, which will likely take several more years to complete, is relatively trivial compared to definitively characterizing the interactions within the proteome.

Non-Static Structure Visualization

Unlike a nucleotide sequence, which is a relatively static structure, proteins are dynamic entities that change their shape and association with other molecules as a function of temperature, chemical interactions, pH, and other changes in the environment.

Why Visualize?

In each area of bioinformatics, the rationale for using graphics instead of tables or strings of data is to shift the user’s mental processing from reading and mathematical, logical interpretation to faster pattern recognition.

molecular simulation

Pattern recognition is an area where humans are much more efficient than computers.

Some Common Tools

100’s of visualization tools have been developed in bioinformatics.

Many are specific to hardware such as microarray devices.

Shareware utilities for PC’s

  • PDB Viewer, WebMol, RasMol, Protein Explorer, Cn3D
  • VMD, MolMol, MidasPlus, Pymol, Chime, Chimera

 Wireframe used to show individual chains:


Stick view showing atoms and bonds:


Surface View showing surface fields:


Ribbon view of secondary structure:


Other properties that can be visualized:

MolMol supports the display of electrostatic potentials across a protein molecule. MidasPlus (a predecessor of Chimera) allows for the editing of sequences visually to see the effects of point mutations.

The field is wide open.

To definitively characterize the interactions within the proteome, we need more tools. We need new metaphors for managing this complex data. We need tools to reveal dynamic relationships.

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