Macromolecular Modeling Blog ™

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RosettaCon 2009 has ended just a few days ago.

This was a very exciting meeting, gathering almost all Rosetta developers from around the world, and representatives of the major industry licensees of Rosetta. The talks were quite diverse, ranging from new Rosetta protocols under development, applications with regards to numerous biological systems, and up to code architecture and future development of the code.

For scientists specializing in a specific field (such as computational structural biology – just off the top of my head) there are rare occasions in which meetings are dedicated entirely to their topic. This was such a conference! All through the three days of conference and one day of hiking, people had talked, discussed, brain stormed, ate, breathed, thought, swam, hiked, mingled and laughed protein structure. If the coffee break was drawn as a comic figure, with bubble clouds to depict thoughts and conversations, it would be a sea of alpha-helices, weird looking loops, rotamers, ligands and co-factors at interfaces, strange folds and stranger rainbow colored cartoon proteins. A modeler’s utopia.
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The 8th community wide experiment on the critical assessment of techniques for protein structure prediction ,or CASP8 for short, has ended a couple of months back, and the results are in. In this CASP, 112 human expert groups were registered and 121 automatic prediction servers. 128 targets were released for prediction, generating a total of 80,560(!) submitted models. 

According to the CASP website, for the human expert groups on 71 template based modeling (TBM) and free modeling (FM) targets, the top three groups were:

1. The Baker Lab
2. The Lithuanian Institute of Biotechnology
3. The Zhang Lab

For the server’s automatic predictions (164 TBM & FM) the top rankings were:

1. The Zhang-server (I-TASSER)
2. RAPTOR
3. ROBETTA (Rosetta server)

FoldIt! is a revolutionary new computer game enabling you to contribute to important scientific research. The goal of this game is to do what we all do on a regular basis – model proteins. Based on the Rosetta Software, FoldIt gives a very intuitive and simple interface to protein folding. The more stable you fold the protein, the better is your score. It relies on the paradigm that computers may be good at doing many many simple calculations quickly, but there is no replacement for human intuition.  

It has recieved much attention when it first aired, by top blogs and newspapers (Such as: Life Hacker,New-scientist,ABC news (SF),Nature Blog,The Economist, NY Times Freakonomics, and more) and is still gaining popularity. Not surprisingly many of the best players are not scientists

As so much has been written about this game, I will not go into its details, In one word: addictive! One of the nicer options of the game is that it enables groups to join efforts in solving the folding puzzles. It is with great pleasure I announce the foramtion of the “Macromolecular Modeling Blog” FoldIt group. 

Think of a group of people who all specialize (or are at least interested.. ) in modeling. We will be an unstoppable power in the FoldIt domain. Polypeptides will yield to our commands, sheets will be torn, helices will bend. For fame and science, our group shall solve any fold! 

Useful links: Download the game, FoldIt introductory video, Join the group!!!

Good luck to us.