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Chu

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Message 31611 - Posted 24 Nov 2006 0:05:19 UTC
Last modified: 24 Nov 2006 0:08:17 UTC

CAPRI more info here -- a blind docking prediction competition which is similar to CASP for structure prediction, has opened for the round 11. In the next two and half weeks, there will be one target to be predicted. For the first time we will create blind docking models using BOINC distributed computing and the job names all start from "CAPRI_11". Thanks for everyone's support and your contribution will increase our chance greatly to identify the correct answer.
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MattDavis
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Message 31644 - Posted 24 Nov 2006 22:24:06 UTC

This project may get an early bump now that Einstein is down for the near future.
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Message 31648 - Posted 25 Nov 2006 1:28:47 UTC

So why does the graphic for the WU currently running say that the native conformation is unknown but still show a native structure?

MattDavis
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Message 31650 - Posted 25 Nov 2006 3:44:44 UTC

I haven't received many of these units - most don't start with "CAPRI_11."

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Message 31653 - Posted 25 Nov 2006 8:15:37 UTC

Still testing them on Ralph
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Message 31655 - Posted 25 Nov 2006 8:45:53 UTC - in response to Message ID 31653.

Still testing them on Ralph


They've made it to Rosetta, though. The WU I mwntioned below starts with "CAPRI_11"

MattDavis
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Message 31661 - Posted 25 Nov 2006 18:35:21 UTC - in response to Message ID 31655.

Still testing them on Ralph


They've made it to Rosetta, though. The WU I mwntioned below starts with "CAPRI_11"


Right, I read the main page message as meaning they were going to be used on Rosetta now. I've received a few but most of my work units don't start with "CAPRI_11."

Chu

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Message 31665 - Posted 25 Nov 2006 19:58:14 UTC - in response to Message ID 31648.

In short, that is not a real native structure, just a randomly chosen referece point we put in.

Unlike the structure prediction where the model is built up from a plain sequence, the docking prediction starts from two independent structures and tries to find the best way by which the two proteins can interact with each other. For this blind docking prediction, we randomly orient two proteins together and just use it as a reference point ( or "pseudo-native" structure). Of course, the RMSD value here does not mean anything and we eventually will select our predicted models by energy and cluster size.

So why does the graphic for the WU currently running say that the native conformation is unknown but still show a native structure?


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Chu

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Message 31666 - Posted 25 Nov 2006 20:03:26 UTC - in response to Message ID 31661.

It is on Rosetta@Home now, but is being added to the queue slowly as they share the queue with other WUs.

Still testing them on Ralph


They've made it to Rosetta, though. The WU I mwntioned below starts with "CAPRI_11"


Right, I read the main page message as meaning they were going to be used on Rosetta now. I've received a few but most of my work units don't start with "CAPRI_11."


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Message 31669 - Posted 25 Nov 2006 22:53:19 UTC

Thanks Chu. I was worried that something had gone wrong with the batch. I'm glad to hear that everything is running according to plan.

mentabelgium

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Message 31684 - Posted 26 Nov 2006 13:37:37 UTC

Received my first Capri 11 workunit today :-)
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Message 32252 - Posted 8 Dec 2006 3:37:34 UTC - in response to Message ID 31665.

For this blind docking prediction, we randomly orient two proteins together and just use it as a reference point ( or "pseudo-native" structure). Of course, the RMSD value here does not mean anything and we eventually will select our predicted models by energy and cluster size.


Just to be redundant I suppose, this means that the RMSD for the WUs that start with "CAPRI_11" in the Active Work Units graphs dont mean anything either, right?

Chu

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Message 32284 - Posted 8 Dec 2006 17:43:49 UTC - in response to Message ID 32252.

Correct.

For this blind docking prediction, we randomly orient two proteins together and just use it as a reference point ( or "pseudo-native" structure). Of course, the RMSD value here does not mean anything and we eventually will select our predicted models by energy and cluster size.


Just to be redundant I suppose, this means that the RMSD for the WUs that start with "CAPRI_11" in the Active Work Units graphs dont mean anything either, right?


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Message 32432 - Posted 10 Dec 2006 23:42:26 UTC - in response to Message ID 32284.

I got 1 CAPRI 11 WU. Wow! exciting stuff!

Who ended up winning this "competition"?

Chu

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Message 32462 - Posted 11 Dec 2006 17:19:46 UTC - in response to Message ID 32432.

It is at the closing stage now and usually one month or two after the submission deadline, we will hear the result from the evaluators. We will post it here as soon as we are notified.

I got 1 CAPRI 11 WU. Wow! exciting stuff!

Who ended up winning this "competition"?


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Tom Philippart
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Message 32464 - Posted 11 Dec 2006 18:05:33 UTC

i didn't get any CAPRI 11 WUs :(
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Message 32506 - Posted 12 Dec 2006 9:44:02 UTC - in response to Message ID 32464.

i didn't get any CAPRI 11 WUs :(


You didn't miss anything.

Message boards : Rosetta@home Science : CAPRI 11 opened


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