Feb
22
2017
0

Only TWO spots left for RosettaCON2017!

RosettaCON2017_edit_slide

There are only TWO spots remaining for RosettaCON2017 for members of the pharmaceutical, biotech, and related industries. Request an invitation through the RosettaCON website.

RosettaCON2017 dates: August 8 – August 11, 2017.

RosettaCON is an annual conference at the Sleeping Lady Mountain Retreat in Washington’s Cascade Mountains, where Rosetta Commons member laboratories share the latest experimental and computational research breakthroughs in protein and macromolecular engineering and structure prediction . The Commons grew out of David Baker’s laboratory at the University of Washington and is now a consortium of over forty international laboratories. Rich Bonneau of New York University, Charlie Strauss of the Los Alamos National Laboratory, Bruno Correia of EPFL of Lausanne, and Vladimir Yarov-Yarovoy of the University of California at Davis organize this year’s conference. We are delighted to have Ian Wilson of The Scripps Research Institute, and Shoshana Wodak of the Vlaamse Institute of Technology (VIB) and the Vrije Universiteit Brussels (VUB) as confirmed guest speakers.

This year’s conference will be featured in a special addition of PLoS. All attendees are invited to contribute to the special edition.

In addition to showcasing cutting edge research, there will be an industry-focused session for fostering collaborations and exploring the exchange of ideas, people and resources. We invite you to participate in this session through presentations, flip charts, and breakout discussions. We hope to expand on the ever-growing number of industry-Rosetta Commons collaborations.

Nov
09
2011
0

Protein design: breaks gluten, wins iGEM2011

An undergraduate group of students from the University of Washington, managed to redesign an enzyme to efficiently break down a model peptide for Gluten, achieving an increase in activity of hundreds fold over the only current clinically tested treatment for Gluten intolerance – Winning iGEM2011. All this, over the summer. Oh, and they also managed to produce Diesel in E. Coli.

(more…)

Written by Nir London in: News,Weird science | Tags: , , , , , ,
Aug
10
2009
0

RosettaCon 2009 – perspective

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.
(more…)

Jan
30
2009
2

CASP8 Results: Human Vs. Servers

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)
Many other assessments exist (Zhang,Baker,Grishin,McGuffin,Cheng) which show quite consistently according to different measures that the Zhang server is ranked first amongst servers, while the Baker group is ranked first for the human/server targets. Is there still some human intuition in protein modeling that can not be formulated into a server ?
Another anecdotal indication for this trend are the FoldIt! players results in CASP8 : for 7 targets, players or groups were ranked amongst the best 3 predictions, and for one target they actually predicted the best model (out of 77 entries).
So the next time you need to model a protein, will you use a server ? or operate a modeling software yourself ?


Written by Nir London in: Weird science | Tags: , , , , , , , , ,
Nov
30
2008
3

FoldIt! – you’re either with us, or against us.

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.  

FoldIt - The protein folding game.

 

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 gameFoldIt introductory video, Join the group!!!

Good luck to us.

Written by Nir London in: Weird science | Tags: , , , , , ,

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