Thursday, April 1, 2010

Google Cell Biology? (RCSB Protein Databank in Google Earth)

Lately, I have been impressed with Google Earth and Maps and have tinkered with some of the JavaScript examples provided on the Google Earth tutorial page.

I must admit that I have been harboring the idea to design a 3D environment which allows biochemists and cellular biologists the ability to navigate the interior of a theoretical cell.

Image traveling around in a cell! A complete cellular spatial layout - traveling from the nuclear envelope to the mitochondria - and having the ability to witness CGI trajectories of enzyme mechanisms and movements. Visually experience the fluid movements of the bi-lipid membrane layer.

How could something like this come to fruition?

It seems that a plausible bridge exists between the information technologies surrounding Google Earth and the bountiful supply of RCSB Protein Data Base files. A software project like this is much larger than a small group of scientists and programmers can handle; however, a vast implementation, perhaps acknowledged by Google, could have have a pivotal advantage for future engineering of "artificial" macromolecular systems.

Looks like I'll be spending the next few days trying to load PDB files into Google Earth.

Timothy Franklin Montague


I have made some progress on importing PDB files into Google Earth!
By this path I was able to convert PDB models into KMZ models:
PDB -> VRML -> 3DS -> KMZ

(1) Using Chimera convert a PDB into VRML
(2) Using Blender (or 3DS Max) convert a VRML into 3DS format
(3) Using Google SketchUp convert 3DS into KMZ format

Check out the following images!


PDB file in Google SketchUp

PDB file in Google Earth!

I will continue to update this post, when I expand this project. Enjoy!

Timothy Franklin Montague