Macromolecular Modeling Blog ™

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.

One of the funniest posts I’ve ever read in the context of protein folding was written by Bosco K. Ho in his “Trapped in the USA” blog. It entails the ten commandments of protein folding which are:

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In this Bi-weekly digest, a structural insight into the inhibition mechanism of calpastatins, analysis of core hydrophobic amino acids interactions and more relevant titles form current issues of molecular and computational biology literature. If you want to initiate in a public discussion on one of these, let us know in the comments.

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Disclaimer: We at “Rosetta Design Group“, use, develop and love Rosetta. That being said, you’d understand our amicable descriptions.

Rosetta is a modeling software suite that can do anything that have to do with modeling. From ab-initio folding and homology modeling, through protein-protein or protein-ligand docking, and to protein and enzyme design. Dozens of papers were written about its different protocols and about their application to specific biological systems. The secret for Rosetta’s success are the Rosetta Commons: a consortium, including over a hundred scientists from over 12 Universities which continues the ongoing research and development of the software.

Every summer the Rosetta Commons researchers, world experts on macromolecular modeling, as well as the people behind the code, gather at the Rosetta Conference (dubbed “RosettaCon”) to exchange ideas and discuss future plans.

We would like to invite you to RosettaCon to participate in workshops, seminars, and to have an opportunity to meet the Rosetta Commons researchers.
RosettaCon will take place during August 4-7 at the beautiful Sleeping Lady Mountain Retreat in Leavenworth, Washington, about 2.5 hours outside Seattle, set amid towering conifers and dramatic mountain scenery.

The Rosetta software is currently licensed for free to users at academic and nonprofit institutions and have over 2000 academic users in more than 32 countries. Commercial entities can use Rosetta by paying a license fee. Amongst past participants in these workshops are representatives of the big pharma companies and Rosetta’s licensees, RosettaCon Workshop 2008 was sponsored by Merck and Nanorex.

If you may be interested in joining us this year, please let me know, We will be sending the preliminary agenda to assess participants preferences in terms of workshop session contents and seminar topics, and to taylor them to your needs.

For more information and registration, email:

nir AT rosettadesigngroup.com

Have you ever read a paper, stumbled upon some random PDB id and was itching to see the structure ? maybe play with it for several minutes ? get a general impression ? but, alas, you were too lazy to actually go the PDB and download the structure! Carson Andorf provides an easy solution in the form of a “PDB Structure Viewer with Sting!” Google Gadget. 

Just enter your PDB id and viola you get an image of the structure another click on the image would let you play around with it. Add this to your iGoogle page and you’ll never shun another molecule again. And while your at it, add the macromolecular modeling blog feed to your iGoogle page as well  :)

What is your favorite google gadget ? Tell us in the comments.

I received an important email alert from NCBI today about a cutting edge, protein science publication by D. Baker. This publication along with the passage of prop 2 in California earlier this month are positive steps towards getting more chicks to become macromolecular modelers.

What is your favorite way of keeping up to date?

S. Gordo et al. implement a new strategy for preventative anti-cancer therapeutics. R337H is the most frequent inherited mutation in p53, “The guardian of the genome”, and is associated with wide spectrum of cancer forms. The mutation is believed to destabilize the native tetramer form of p53. In this study the researchers designed a small molecule that reconstitutes tetramerization of such a mutant. By Nir London.

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In this Bi-Weekly digest – relevant titles form current issues of molecular and computational biology literature, amongst featured titles: Surface Sites for Engineering Allosteric Control in Proteins and The RNA Polymerase ”Switch Region” Is a Target for Inhibitors. If you want to initiate in a public discussion on one of these, let us know in the comments.

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The task of predicting the interface of a given protein using only the structure of the unbound protein, is an important goal. Many groups have attempted tackling this problem from different fronts and using different approaches. We preset here 10 popular protein-protein interface prediction servers. This might prove especially helpful to those who take part in the ongoing CAPRI round.

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