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Molecular Visualisation
by Juan C. Dürsteler [message nº 76]

One of the most active areas of bioinformatics is that of molecular visualisation. A key topic in the design of new drugs, it’s evolving in order to make the extreme complexity of this field more understandable .

MolVisStereo.jpg (25834 bytes)
Estereoscopic pair: Click on the image to enlarge it and defocus your eyes until both images fuse into one. Then you can see the molecule floating in 3D space.
(Courtesy of Accelrys)
MolVisHeme.jpg (35056 bytes)
Heme molecule. On top of the ball and stick representation, a ribbon representation of Heme bound to a protein is placed. Click on the image to enlarge it.
(Courtesy of Accelrys)

Molecule design is one of the bases of today’s pharmaceutical industry. You probably still remember the balls and sticks used in secondary school to teach the structure of molecules in the classroom of Chemistry. The balls symbolised atoms and the sticks were the bonds.

This 3D representation in the real world had interesting properties: it let you have an idea of the 3D structure of the molecules and a better understanding of the way bonds are placed. It even let you recognise that certain geometries were impossible. Moreover you could “touch and feel” the molecule.

As you already know, new drug design is far more complex. Here what is of our interest is not only the visualisation of molecules but that of their properties, like electron density, the layout of the Van der Waals forces, etc. 

In the enclosed figures you can see some examples, including a stereoscopic image viewable without any special glasses.

The designer of molecules is interested in sophisticated aspects like the internal areas of the molecules that can be reached by a solvent, the shape of the electronic orbitals or the zones where hydrophobic interactions can occur. The things that determine the properties of the molecule.

This type of information typically has 4 or more dimensions. For this reason it’s typically represented as iso-surfaces of certain parameters (like contour lines in a topographic map but in 3D). In order to better visualise the geometry, stereo pairs are generated, allowing you to see the molecule with stereoscopic vision, appreciating the depth.

Despite being a great advantage, visualisation systems are insufficient to cope with the complexity of the problem and they are, sometimes, difficult to understand even for experts on the topic.

For this reason in this field, like in many others related with visualisation, an increasing interest in the use of multi-modal interfaces has been growing in the last years, combining different senses like touch and hearing in order to create a more or less complete experience of the interaction that allows you to build a better intuition.

This way a haptic system with force-feedback, able to exert a force in response to the interaction with the design software, allows us to “touch” the molecules, sense its active sites, the zones where a bond with other molecule can take place, etc. 

The addition of sounds related to the state of our actions and to the properties of the molecule enrich the experience even more, allowing us to “hear” the properties of the same, contributing to create an integrated sensation around the interaction with the molecule.

Multi-modal interfaces are still in their infancy, but in the future they will have a lot to say, especially in fields where the complexity of the elements to visualise could benefit from the richness that they provide.


Nowadays there are many molecule visualisation systems, both commercial and freeware. Among the latter you can find Protein Explorer  an improved version of the classical RasMol, free software created by Eric Martz from Massachussets University. It’s widespread in the academic community, used for educational and research purposes.

In terms of the commercial software you can find, among others, Gaussian or Accelrys that produces high quality graphics.

Links of this issue:

http://www.umass.edu/microbio/chime/explorer/  
http://www.gaussian.com  
http://www.accelrys.com/  
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