As well as the Pubchem site for small molecules there are the protein database sites, such as the RSBC site, that have structural data for proteins and other macromolecules. I made a parser for the PDB files that these sites provide. There is a WebGL version and a Flash version of a DNA molecule below.
Using the Three.Js library.
Using the Adobe Proscenium library.
In the previous post I used the WebGL library three.js to produce a 3D space-filling model of serotonin. Without getting into a silly HTML5 vs Flash war, I have produced the same model with Flash Stage3d using the Away3d library. In a future post I’ll explain the advantages and problems of using Flash or WebGL, but for now, serotonin Flash style.
You will need Flash Player 11 or greater
Visualising the structure of molecules in 3D on the web is useful for education and other communication activities. Web-based java and HTML5 viewers exist that allow this. However, I think that gaming technologies will allow models to be used in more sophisticated learning objects where users can select and highlight specific structural or functional regions of the molecules. This will enhance the learner’s experience and make it more immersive.
I have used WebGL, Flash and Unity3D, all 3D technologies that are popular with online gaming developers, to visualise molecules.