Wednesday, June 20, 2007

Molecule Docking in Second Life

Update: Hiro posted a YouTube video of the docking - see end of post

A while back, I posted about how we have been experimenting with representing our research work on UsefulChem in Second Life. With the help of Andrew Lang (Hiro Sheridan on SL), we put up one of the molecules that we had been trying to make as an anti-malarial compound.

Hiro has now taken this to the next level and has the molecule actually moving into the binding pocket of the targeted enzyme (enoyl reductase) upon clicking on it. There are 4 hydrogen-bonding interactions between the molecules and the atoms involved are tagged in green.

I'm grateful that Hiro took the time to show the self-docking animation because it is really hard to manually connect these two 3D puzzle pieces in Second Life (give it a try! - slurl).

In order to get to this point required a considerable amount of collaboration and I would like to thank everyone involved: Goeff Hutchison, Keith Davies, Sean Gardner, Tsu-Soo Tan and Eloise Pasteur.


At 4:25 PM, Blogger Egon Willighagen said...

It's a shame that each time I got to Second Nature or Drexel Island no one is there... :(

At 8:09 PM, Blogger Science & Science Ficiton said...

There's three people on Drexel right now and Second Nature has had over 600 visitors in the last 30 days. If you'd like a tour, IM Horace Moody for Drexel or Joanna Wombat for Second Nature.

I just posted a video of the molecule docking on youtube:

Too see it for yourself go here:

At 6:09 AM, Blogger Jean-Claude Bradley said...

Hiro - thanks for posting the video!
Egon - well you'll have to keep coming back. I've got you in my friend list now so we'll connect in SL soon.


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