Interactive 3D Visualisations of Biological Molecules Integrated into the Scholarly Literature

The embargo has now been lifted on the announcement from PLoS ONE - partially reproduced here:

On October 20th 2009, PLoS ONE will feature an impressive new 3D molecular animation technology on five newly published articles. This represents the start of a new PLoS ONE collection entitled “Structural Biology and Human Health: Medically Relevant Proteins from the SGC” (also known as the ‘Structural Genomics Consortium’).

These peer-reviewed articles, which include some of the research highlights from the SGC, describe new protein structures, including a protein involved in the survival and proliferation of cancer cells, a protein associated with hereditary paraplegia, and a protein involved in degrading foreign compounds and pollutants in the body.

Readers of these enhanced articles will first need to download a free plug-in for their browser but will then be able to click on hyperlinked text within the article to ‘fly’ to the relevant position within the molecule, and to then interact with it at will (by zooming, rotating and exploring). The functionality, whereby the text of an academic article is tightly integrated with an animated and interactive molecular structure, provides an entirely new and enhanced experience with a significant “wow” factor.

The first enhanced articles are available here. I've been trying to evaluate these but I'm having trouble downloading the required plug-in: it is very slow and has just stalled on me. Maybe the problem is on my side so I'm asking the community to give these a spin and report. I am especially curious about the comparison with Jmol. This particular plug-in does not use Java at all from what I can glean from the press release.

Notwithstanding these probably temporary issues I think this is a very exciting development for scientific publication in the life sciences.

Campus Technology Article about Molecules in Second Life

Linda Briggs wrote a nice article in Campus Technology about using Second Life to teach and highlighted the chemistry application that I used last term:

Creating Life-Size Molecules in Second Life

A Conversation with Drexel University's Jean-Claude Bradley

1/9/2008

By Linda L Briggs

CT: Conversely, what are some things that work really well in Second Life?

JCB: One thing new that I've done this term is have students do a project in Second Life.

CT: Yes, you recently wrote in your blog that one of your students created a life-size model of a molecule as part of that. That sounded really cool.

JCB: Right. To be able to stand next to a molecule that is as tall as you are, and to have your teacher be able to walk around it with you and comment,... that's pretty useful.

[....]

CT: Do you have advice for instructors who want to integrate Second Life into their course?

JCB: You should have a really good reason to do it. The best advice is to find another teacher who is actually using it, and try to experience what the student is experiencing. You'll get some ideas and advice from that. I was just talking to another teacher an hour ago who might be doing some things in Second Life. She's also an organic chemistry teacher. I told her, just send your students to Drexel Island; have them interact with my students, click around on the quizzes, and if you think it might make sense, you can spawn off from that.

A lot of people have bad experiences in Second Life because they don't have a good reason for going there. It's like having people go to the Internet without a Web address. You want to be guided. That's the best possible scenario.

It's just another tool. I wouldn't teach exclusively on Second Life. We have WebCT Blackboard; I have my wiki; I have my blogs; and those things all have their strengths. You've got to leverage them all.

Drexel Island also got a mention in Matt Villano's article in Campus Technology: 13 Tips for Virtual World Teaching

Indexing Molecules in Second Life

As I've recently commented, there has been media interest in the use of the virtual online world Second Life for chemistry. We also recently demonstrated on Drexel Island that it was possible to visualize molecular docking using the molecular rezzer developed by Andrew Lang.

Nature Island also hosts several common molecules, including buckyballs. As more people start to experiment with representing chemicals and chemistry research in Second Life it would be nice if such examples were discovered by a simple Google search.

All that really needs to be done to accomplish this is to co-locate molecular descriptors with corresponding SLURLs (Second Life URLs) on the same web page. When clicked, the SLURL will automatically start Second Life and teleport the user to the location where the molecule can be found. If the user does not have Second Life, a page pops up explaining how to set up a free account and download the software. This could be a good way to introduce the mainstream chemical community to new modalities of communicating science.

As for descriptors, I am suggesting that we use InChIs and common names at the very least. Google does a fairly good job of finding molecules by InChI.

I created a wiki,
http://secondlifemolecules.wikispaces.com/
and seeded it with a molecule from our malaria research that I've used in several places and with caffeine, which is displayed on Nature Island. I invite anyone to contribute to the wiki and add information that could be useful. (The indexing on Google can take a few days for a new wiki)

There are several other ways of creating this index and I think the more redundancy the better. For example, we could make Second Life a "supplier" on ChemSpider. It might also be possible for Andrew's molecule rezzer to note the location of a molecule when it gets created in Second Life and automatically send off an email to a Blogger account to create a post.



Chemical Blogspace Tags

InChI=1/C8H10N4O2/c1-10-4-9-6-5(10)7(13)12(3)8(14)11(6)2/h4H,1-3H3
caffeine