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: , , , , , ,
Nov
28
2008
0

The Ten Commandments Of Protein Folding

 

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:

(more…)

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

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