BioVRML, VRML in Biochemistry

Molecules, protiens, chemical bonding, don't all those biochemical terms just bring a chill up your spine? Ok maybe not. But for those people who do have a burning desire to see what these molecules look like and how they move, VRML is a wonderful, and free, way to visualize them. Certainly the pioneer of VRML molecular imaging are the folks of the Department of Physical Chemistry at the Darmstadt University of Technology in Germany. Their web page titled "VRML in Chemistry" with the paper "VRML for the communication with 3D scenarios of biomolecules" let's users select from hundreds of molecules and protiens which can be displayed in several forms. Molecules can be viewed using stick, ball and stick, space filling representations. Some of the VRML files even contain VRML objects they call "space buttons" (click on the image on the top of this article for one such world) to control the information and type of display.

The Darmstadt folks wisely chose to write a converter, PDB-to-VRML, which converts files in the PDF format, a widely used protein format, and VRML. There exist large databases of protiens, such as the Brookhaven Protein Databank used by the biotechnology research and commercial communities. One of the few "industrial strength" uses of VRML is as a visualization of the molecules in this important international database. If you search for a protein you can retrieve a VRML molecule visualization.

The latest Darmstadt contribution is a collection of VRML models that move. Using the capabilities of VRML 2 this page illustrates the motion of molecules for the selected frequencies. Last but not least, from Darmstadt, is a web page on the use of VRML for Cancer research. This web page titled "VRML in Cancer Research: Local Changes in Binding Properties of Wild Type and Mutated p53 Tumor Suppressor Protein" by M. Keil, G. Moeckel, J. Brickmann presents a half dozen VRML worlds as visualizations of various affects of cancer on the p53 gene mutations.

The use of chemical data types on the Internet in general has grown to such a degree that a collection of MIME types specifically for chemistry exists. These MIME types encode representations for proteins (.pdb), crystallographic information (.cif), nucleotides (.emb) and lots more.

When building a good VRML chemistry application, one should first see what models already exist. The people at OCNUS have some chemical molecules for clip art. They feature caffeine, ethanol and the always popular nutrasweet. If your feeling a little hungry and in need of some amino acids for your VRML diet, check out the Image Library of Biological Macromolecules (IMB) with it's collection of the 20 Standard Amino Acids. Don't stop just at Amino Acids though check out the IMB's Virtual Reality Division with VRML models of Nucleotides, Proteins, RNA, DNA, and Carbohydrates. It's a veritable smorgasbord of VRML biochemical models. Well that's about it for this week, all this talk of proteins and carbohydrates are making me hungry.

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