Oct
21
2012
0

CASP10 conference

Critical Assessment of Protein Structure Prediction *CASP10* (an EMBO conference)
9-12 December 2012 | Gaeta, Italy

Every two years since 1994 CASP has conducted a community wide experiment to assess the state of the art in protein structure modeling.
The 2012 conference will report the results of 10th experiment and celebrate progress over almost 20 years of monitoring the field.

(more…)

Jul
15
2010
1

2010 Cryo-EM Modeling challenge

Cryo-EM single particle analysis is a method for determining structures of large molecules and macromolecular assemblies at resolutions ranging from 3.5- 30 A. Interpreting the density maps produced by this technique represents an ongoing challenge, for which molecular modeling techniques offer some unique solutions.

Over the last five years, cryo-EM single particle analysis has begun producing structures at resolutions better than 5 A, with subnanometer resolutions becoming common. At resolutions between 5 and 9 A it becomes possible to move beyond simple rigid-body docking and alter atomistic models to reposition helices and sheets, to better fit the cryo-EM based density maps. At 3-5 A resolution de-novo C-alpha traces and in some cases full atomistic models can be constructed directly from the cyro-EM density without invoking x-ray crystallography.

We call this a challenge rather than a contest because, unlike CASP, there is no hidden answer to be revealed. In this project, we provide publicly available cryo-EM densities for a selected set of structures at different resolutions, and challenge those in the modeling community to apply their tools to extract as much information as they can from each. At the end, the results will be evaluated by comparing the results of different groups, and validating against any other existing knowledge about each target. We hope this will yield new insights into these published structures, and at the very least, it will establish the capabilities of current modeling methods, and give the cryo-EM community some guidance as to how to proceed with maps in various resolution ranges. For modelers it provides a new area in which to apply/develop their techniques, and demonstrating your tools’ capabilities may lead to new opportunities for collaboration.

Please see the challenge website for more details.

Written by Nir London in: Uncategorized | Tags: , , , ,
Jan
11
2010
2

CAPRI or: What is the State of Protein-Protein Docking?

This is the first post in a series, summarizing the CAPRI (Critical Assessment of PRediction of Interactions) 4th Evaluation meeting. In this post I’ll try to give a more personal perspective of the experiment results, the state and trends of computational protein-protein docking and the vibes behind the scenes. The next posts in the series will shortly summarize select talks from the meeting, kindly provided by the speakers.

(more…)

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

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