Apr
29
2013
0

CAPRI 5th evaluation meeting

The CAPRI 5th evaluation meeting has just finished last week.

Unfortunately I couldn’t attend this year.

Fortunately, you can get the spirit of the meeting from this series of 3 blog posts over at Grid-Cast:

Combining and conquering at the CAPRI 5th evaluation meeting

Proteins by design – expanding on nature

Wrapping up at CAPRI – beers, bikes and brainstorming

The current CAPRI round is all about peptide docking! Exciting!

If anyone came back from the meeting please share your impressions.

Written by Nir London in: Events | Tags: , ,
Feb
28
2010
0

CAPRI: Selected Talks IV

This is the fifth and last post in the CAPRI series, summarizing the presentations of Xiaoqin Zou and Ora Schueler-Furman (Saving the best for last..), as provided by the speakers. I hope the CAPRI series was able to give a snapshot of the state of computational protein-protein docking and its community. I want to thank again to everyone that took part in the meeting and helped me with this series.

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Jan
30
2010
1

CAPRI: Selected Talks III

This is the fourth post in the CAPRI series, summarizing the presentations of Paul Bates, Martin Zacharias, and Carlos Camacho, as provided by the speakers. More to appear in the continuation of the series.

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Jan
17
2010
0

CAPRI: Selected Talks II

This is the third post in the CAPRI series, summarizing the presentations of Jeffrey Gray, Zhiping Weng, and Miriam Eisenstein, as provided by the speakers. More to appear in the continuation of the series.
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Jan
12
2010
0

CAPRI: Selected Talks I

This is the second post in the CAPRI series, summarizing the presentations of Sandor Vajda, Alexandre Bonvin, and Julie Mitchell, as provided by the speakers. More to appear in the continuation of the series.

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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.

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Written by Nir London in: Events,Weird science | Tags: , , , ,
Mar
30
2009
0

Protein-Protein Docking on the rise.

We have recently conducted a poll amongst people interested in learning more about the Rosetta software (as a preliminary step to the Rosetta Academic Training Workshop). One of the questions in that poll was: “Which Rosetta related topics is of the most interest to you?” The results (from ~200 participants) are summarized in the graph below.

 

Interest trends amongst Rosetta users

Interest trends amongst Rosetta users

 

Protein-protein docking was chosen as the topic with the highest interest level, with a slight gap from ab-initio structure prediction and protein-ligand docking. This correlates well with another superficial analysis we made a while back (What’s trendy in structural bioinformatics) in which we showed qualitatively that docking receives the most interest from ‘Cite U Like‘ structural bioinformaticians. It is worth noting that Molecular Dynamics was not included, since Rosetta is not intended for MD simulations.

What is your field in structural bioinformatics? Anyone has more evidence for the increase in interest in protein-protein docking?

Oct
31
2008
3

Incorporating Flexibility Into Docking Using Normal Mode Analysis

Incorporation of flexibility into docking simulations and accounting for backbone conformational changes during association is probably the toughest problem protein-protein dockers are facing today. Normal Mode Analysis is lately the answer of many groups to this problem. We hereby review two approaches of incorporating NMA into docking simulations, reflecting the induced fit vs. conformational sampling association mechanisms. 

(more…)

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