Rosetta Application Version Release Log

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Mike Tyka

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Message 64479 - Posted: 15 Dec 2009, 1:22:39 UTC

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Profile David E K
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Message 64950 - Posted: 13 Jan 2010, 18:08:36 UTC

Minirosetta has been updated to 2.05.

This version includes a fix to checkpointing for a specific type of job, and other minor updates.
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Message 64954 - Posted: 13 Jan 2010, 19:47:34 UTC

Hello,

There were very interesting questions on the boards regarding this new protein-interface design run, particularly with respect to checkpointing, so below is an explanation that is somewhat more technical.

The aim of this project is to redesign a protein that would inhibit a pathogen (see https://boinc.bakerlab.org/forum_thread.php?id=4477). The computational strategy that we've implemented looks for an exquisite and very rare geometric relationship between amino acid residues on the surface of the redesigned protein and the target pathogenic protein. The method can very quickly go through multiple starting points and triage most of them. Those that pass this triaging step are then subjected to rounds of design.

Often people explain the problem of protein folding as an energy landscape in which you're trying to identify minima corresponding to stable structures. Due to the rarity of the combination of amino acid conformations that we're looking for the energy landscape might be best described as a golf course: a few good conformations are scattered across a vast and bland space. The rarity of these points and the vastness of the space make the huge processing power of ROSETTA @ HOME an ideal place to identify these putative binders.

Since each simulation -even fruitful ones- are quite short, in-trajectory checkpointing does not seem necessary at this point (and would probably increase the disk-writing load unnecessarily). With release 2.05 the between-trajectory checkpointing issue should be resolved.
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Message 65734 - Posted: 12 Apr 2010, 18:38:50 UTC

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Message 65841 - Posted: 26 Apr 2010, 19:39:48 UTC

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Message 66049 - Posted: 10 May 2010, 19:47:02 UTC

minirosetta 2.14 is out
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Message 67781 - Posted: 21 Sep 2010, 21:57:04 UTC

minirosetta 2.15 is out. see here for the update
https://boinc.bakerlab.org/rosetta/forum_thread.php?id=5453
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Message 68005 - Posted: 9 Oct 2010, 20:16:31 UTC

minirosetta is reverted to 2.14 (now 2.16)
https://boinc.bakerlab.org/rosetta/forum_thread.php?id=5475
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Message 68307 - Posted: 31 Oct 2010, 23:45:19 UTC

minirosetta is updated to 2.17 to fix the memory and invalidation errors.
https://boinc.bakerlab.org/rosetta/forum_thread.php?id=5502
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Message 75494 - Posted: 26 Apr 2013, 23:04:48 UTC

minirosetta is updated to 3.46 with new development and bug fixes.
https://boinc.bakerlab.org/rosetta/forum_thread.php?id=6222
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Message boards : Number crunching : Rosetta Application Version Release Log



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